MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

PubMed

Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

NASA Astrophysics Data System (ADS)

Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C.

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

SnopViz, an interactive snow profile visualization tool

NASA Astrophysics Data System (ADS)

Fierz, Charles; Egger, Thomas; gerber, Matthias; Bavay, Mathias; Techel, Frank

2016-04-01

SnopViz is a visualization tool for both simulation outputs of the snow-cover model SNOWPACK and observed snow profiles. It has been designed to fulfil the needs of operational services (Swiss Avalanche Warning Service, Avalanche Canada) as well as offer the flexibility required to satisfy the specific needs of researchers. This JavaScript application runs on any modern browser and does not require an active Internet connection. The open source code is available for download from models.slf.ch where examples can also be run. Both the SnopViz library and the SnopViz User Interface will become a full replacement of the current research visualization tool SN_GUI for SNOWPACK. The SnopViz library is a stand-alone application that parses the provided input files, for example, a single snow profile (CAAML file format) or multiple snow profiles as output by SNOWPACK (PRO file format). A plugin architecture allows for handling JSON objects (JavaScript Object Notation) as well and plugins for other file formats may be added easily. The outputs are provided either as vector graphics (SVG) or JSON objects. The SnopViz User Interface (UI) is a browser based stand-alone interface. It runs in every modern browser, including IE, and allows user interaction with the graphs. SVG, the XML based standard for vector graphics, was chosen because of its easy interaction with JS and a good software support (Adobe Illustrator, Inkscape) to manipulate graphs outside SnopViz for publication purposes. SnopViz provides new visualization for SNOWPACK timeline output as well as time series input and output. The actual output format for SNOWPACK timelines was retained while time series are read from SMET files, a file format used in conjunction with the open source data handling code MeteoIO. Finally, SnopViz is able to render single snow profiles, either observed or modelled, that are provided as CAAML-file. This file format (caaml.org/Schemas/V5.0/Profiles/SnowProfileIACS) is an international standard to exchange snow profile data. It is supported by the International Association of Cryospheric Sciences (IACS) and was developed in collaboration with practitioners (Avalanche Canada).

Informatics in radiology (infoRAD): Vendor-neutral case input into a server-based digital teaching file system.

PubMed

Kamauu, Aaron W C; DuVall, Scott L; Robison, Reid J; Liimatta, Andrew P; Wiggins, Richard H; Avrin, David E

2006-01-01

Although digital teaching files are important to radiology education, there are no current satisfactory solutions for export of Digital Imaging and Communications in Medicine (DICOM) images from picture archiving and communication systems (PACS) in desktop publishing format. A vendor-neutral digital teaching file, the Radiology Interesting Case Server (RadICS), offers an efficient tool for harvesting interesting cases from PACS without requiring modifications of the PACS configurations. Radiologists push imaging studies from PACS to RadICS via the standard DICOM Send process, and the RadICS server automatically converts the DICOM images into the Joint Photographic Experts Group format, a common desktop publishing format. They can then select key images and create an interesting case series at the PACS workstation. RadICS was tested successfully against multiple unmodified commercial PACS. Using RadICS, radiologists are able to harvest and author interesting cases at the point of clinical interpretation with minimal disruption in clinical work flow. RSNA, 2006

Developing a radiology-based teaching approach for gross anatomy in the digital era.

PubMed

Marker, David R; Bansal, Anshuman K; Juluru, Krishna; Magid, Donna

2010-08-01

The purpose of this study was to assess the implementation of a digital anatomy lecture series based largely on annotated, radiographic images and the utility of the Radiological Society of North America-developed Medical Imaging Resource Center (MIRC) for providing an online educational resource. A series of digital teaching images were collected and organized to correspond to lecture and dissection topics. MIRC was used to provide the images in a Web-based educational format for incorporation into anatomy lectures and as a review resource. A survey assessed the impressions of the medical students regarding this educational format. MIRC teaching files were successfully used in our teaching approach. The lectures were interactive with questions to and from the medical student audience regarding the labeled images used in the presentation. Eighty-five of 120 students completed the survey. The majority of students (87%) indicated that the MIRC teaching files were "somewhat useful" to "very useful" when incorporated into the lecture. The students who used the MIRC files were most likely to access the material from home (82%) on an occasional basis (76%). With regard to areas for improvement, 63% of the students reported that they would have benefited from more teaching files, and only 9% of the students indicated that the online files were not user friendly. The combination of electronic radiology resources available in lecture format and on the Internet can provide multiple opportunities for medical students to learn and revisit first-year anatomy. MIRC provides a user-friendly format for presenting radiology education files for medical students. 2010 AUR. Published by Elsevier Inc. All rights reserved.

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2017-01-01

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5. PMID:28649160

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-02-13

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments

NASA Astrophysics Data System (ADS)

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-02-01

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon- HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon- HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon- HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

PySE: Python Source Extractor for radio astronomical images

NASA Astrophysics Data System (ADS)

Spreeuw, Hanno; Swinbank, John; Molenaar, Gijs; Staley, Tim; Rol, Evert; Sanders, John; Scheers, Bart; Kuiack, Mark

2018-05-01

PySE finds and measures sources in radio telescope images. It is run with several options, such as the detection threshold (a multiple of the local noise), grid size, and the forced clean beam fit, followed by a list of input image files in standard FITS or CASA format. From these, PySe provides a list of found sources; information such as the calculated background image, source list in different formats (e.g. text, region files importable in DS9), and other data may be saved. PySe can be integrated into a pipeline; it was originally written as part of the LOFAR Transient Detection Pipeline (TraP, ascl:1412.011).

Automated Big Data Analysis in Bottom-up and Targeted Proteomics

PubMed Central

van der Plas-Duivesteijn, Suzanne; Domański, Dominik; Smith, Derek; Borchers, Christoph; Palmblad, Magnus; Mohamme, Yassene

2014-01-01

Similar to other data intensive sciences, analyzing mass spectrometry-based proteomics data involves multiple steps and diverse software using different algorithms and data formats and sizes. Besides that the distributed and evolving nature of the data in online repositories, another challenge is that a scientists have to deal with many steps of analysis pipelines. A documented data processing is also becoming an essential part for the overall reproducibility of the results. Thanks to different e-Science initiatives, scientific workflow engines have become a means for automated, sharable and reproducible data processing. While these are designed as general tools, they can be employed to solve different challenges that we are facing in handling our Big Data. Here we present three use cases: improving the performance of different spectral search engines by decomposing input data and recomposing the resulting files, building spectral libraries from more than 20 million spectra, and integrating information from multiple resources to select most appropriate peptides for targeted proteomics analyses. The three use cases demonstrate different challenges in exploiting proteomics data analysis. In the first we integrate local and cloud processing resources in order to obtain better performance resulting in more than 30-fold speed improvement. By considering search engines as legacy software our solution is applicable to multiple search algorithms. The second use case is an example of automated processing of many data files of different sizes and locations, starting with raw data and ending with the final, ready-to-use library. This demonstrates the robustness and fault tolerance when dealing with huge amount data stored in multiple files. The third use case demonstrates retrieval and integration of information and data from multiple online repositories. In addition to the diversity of data formats and Web interfaces, this use case also illustrates how to deal with incomplete data.

Adobe acrobat: an alternative electronic teaching file construction methodology independent of HTML restrictions.

PubMed

Katzman, G L

2001-03-01

The goal of the project was to create a method by which an in-house digital teaching file could be constructed that was simple, inexpensive, independent of hypertext markup language (HTML) restrictions, and appears identical on multiple platforms. To accomplish this, Microsoft PowerPoint and Adobe Acrobat were used in succession to assemble digital teaching files in the Acrobat portable document file format. They were then verified to appear identically on computers running Windows, Macintosh Operating Systems (OS), and the Silicon Graphics Unix-based OS as either a free-standing file using Acrobat Reader software or from within a browser window using the Acrobat browser plug-in. This latter display method yields a file viewed through a browser window, yet remains independent of underlying HTML restrictions, which may confer an advantage over simple HTML teaching file construction. Thus, a hybrid of HTML-distributed Adobe Acrobat generated WWW documents may be a viable alternative for digital teaching file construction and distribution.

Adding Data Management Services to Parallel File Systems

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

Brandt, Scott

2015-03-04

The objective of this project, called DAMASC for “Data Management in Scientific Computing”, is to coalesce data management with parallel file system management to present a declarative interface to scientists for managing, querying, and analyzing extremely large data sets efficiently and predictably. Managing extremely large data sets is a key challenge of exascale computing. The overhead, energy, and cost of moving massive volumes of data demand designs where computation is close to storage. In current architectures, compute/analysis clusters access data in a physically separate parallel file system and largely leave it scientist to reduce data movement. Over the past decadesmore » the high-end computing community has adopted middleware with multiple layers of abstractions and specialized file formats such as NetCDF-4 and HDF5. These abstractions provide a limited set of high-level data processing functions, but have inherent functionality and performance limitations: middleware that provides access to the highly structured contents of scientific data files stored in the (unstructured) file systems can only optimize to the extent that file system interfaces permit; the highly structured formats of these files often impedes native file system performance optimizations. We are developing Damasc, an enhanced high-performance file system with native rich data management services. Damasc will enable efficient queries and updates over files stored in their native byte-stream format while retaining the inherent performance of file system data storage via declarative queries and updates over views of underlying files. Damasc has four key benefits for the development of data-intensive scientific code: (1) applications can use important data-management services, such as declarative queries, views, and provenance tracking, that are currently available only within database systems; (2) the use of these services becomes easier, as they are provided within a familiar file-based ecosystem; (3) common optimizations, e.g., indexing and caching, are readily supported across several file formats, avoiding effort duplication; and (4) performance improves significantly, as data processing is integrated more tightly with data storage. Our key contributions are: SciHadoop which explores changes to MapReduce assumption by taking advantage of semantics of structured data while preserving MapReduce’s failure and resource management; DataMods which extends common abstractions of parallel file systems so they become programmable such that they can be extended to natively support a variety of data models and can be hooked into emerging distributed runtimes such as Stanford’s Legion; and Miso which combines Hadoop and relational data warehousing to minimize time to insight, taking into account the overhead of ingesting data into data warehousing.« less

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

PubMed

Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

2011-08-15

The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.

EBR-II and TREAT Digitization Project

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

Griffith, George W.; Rabiti, Cristian

2015-09-01

Digitizing the technical drawings for EBR-II and TREAT provides multiple benefits. Moving the scanned or hard copy drawings to modern 3-D CAD (Computer Aided Drawing) format saves data that could be lost over time. The 3-D drawings produce models that can interface with other drawings to make complex assemblies. The 3-D CAD format can also include detailed material properties and parametric coding that can tie critical dimensions together allowing easier modification. Creating the new files from the old drawings has found multiple inconsistencies that are being flagged or corrected improving understanding of the reactor(s).

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

User-Friendly Data Servers for Climate Studies at the Asia-Pacific Data-Research Center (APDRC)

NASA Astrophysics Data System (ADS)

Yuan, G.; Shen, Y.; Zhang, Y.; Merrill, R.; Waseda, T.; Mitsudera, H.; Hacker, P.

2002-12-01

The APDRC was recently established within the International Pacific Research Center (IPRC) at the University of Hawaii. The APDRC mission is to increase understanding of climate variability in the Asia-Pacific region by developing the computational, data-management, and networking infrastructure necessary to make data resources readily accessible and usable by researchers, and by undertaking data-intensive research activities that will both advance knowledge and lead to improvements in data preparation and data products. A focus of recent activity is the implementation of user-friendly data servers. The APDRC is currently running a Live Access Server (LAS) developed at NOAA/PMEL to provide access to and visualization of gridded climate products via the web. The LAS also allows users to download the selected data subsets in various formats (such as binary, netCDF and ASCII). Most of the datasets served by the LAS are also served through our OPeNDAP server (formerly DODS), which allows users to directly access the data using their desktop client tools (e.g. GrADS, Matlab and Ferret). In addition, the APDRC is running an OPeNDAP Catalog/Aggregation Server (CAS) developed by Unidata at UCAR to serve climate data and products such as model output and satellite-derived products. These products are often large (> 2 GB) and are therefore stored as multiple files (stored separately in time or in parameters). The CAS remedies the inconvenience of multiple files and allows access to the whole dataset (or any subset that cuts across the multiple files) via a single request command from any DODS enabled client software. Once the aggregation of files is configured at the server (CAS), the process of aggregation is transparent to the user. The user only needs to know a single URL for the entire dataset, which is, in fact, stored as multiple files. CAS even allows aggregation of files on different systems and at different locations. Currently, the APDRC is serving NCEP, ECMWF, SODA, WOCE-Satellite, TMI, GPI and GSSTF products through the CAS. The APDRC is also running an EPIC server developed by PMEL/NOAA. EPIC is a web-based, data search and display system suited for in situ (station versus gridded) data. The process of locating and selecting individual station data from large collections (millions of profiles or time series, etc.) of in situ data is a major challenge. Serving in situ data on the Internet faces two problems: the irregularity of data formats; and the large quantity of data files. To solve the first problem, we have converted the in situ data into netCDF data format. The second problem was solved by using the EPIC server, which allows users to easily subset the files using a friendly graphical interface. Furthermore, we enhanced the capability of EPIC and configured OPeNDAP into EPIC to serve the numerous in situ data files and to export them to users through two different options: 1) an OPeNDAP pointer file of user-selected data files; and 2) a data package that includes meta-information (e.g., location, time, cruise no, etc.), a local pointer file, and the data files that the user selected. Option 1) is for those who do not want to download the selected data but want to use their own application software (such as GrADS, Matlab and Ferret) for access and analysis; option 2) is for users who want to store the data on their own system (e.g. laptops before going for a cruise) for subsequent analysis. Currently, WOCE CTD and bottle data, the WOCE current meter data, and some Argo float data are being served on the EPIC server.

Emerging Geospatial Sharing Technologies in Earth and Space Science Informatics

NASA Astrophysics Data System (ADS)

Singh, R.; Bermudez, L. E.

2013-12-01

Emerging Geospatial Sharing Technologies in Earth and Space Science Informatics The Open Geospatial Consortium (OGC) mission is to serve as a global forum for the collaboration of developers and users of spatial data products and services, and to advance the development of international standards for geospatial interoperability. The OGC coordinates with over 400 institutions in the development of geospatial standards. In the last years two main trends are making disruptions in geospatial applications: mobile and context sharing. People now have more and more mobile devices to support their work and personal life. Mobile devices are intermittently connected to the internet and have smaller computing capacity than a desktop computer. Based on this trend a new OGC file format standard called GeoPackage will enable greater geospatial data sharing on mobile devices. GeoPackage is perhaps best understood as the natural evolution of Shapefiles, which have been the predominant lightweight geodata sharing format for two decades. However the format is extremely limited. Four major shortcomings are that only vector points, lines, and polygons are supported; property names are constrained by the dBASE format; multiple files are required to encode a single data set; and multiple Shapefiles are required to encode multiple data sets. A more modern lingua franca for geospatial data is long overdue. GeoPackage fills this need with support for vector data, image tile matrices, and raster data. And it builds upon a database container - SQLite - that's self-contained, single-file, cross-platform, serverless, transactional, and open source. A GeoPackage, in essence, is a set of SQLite database tables whose content and layout is described in the candidate GeoPackage Implementation Specification available at https://portal.opengeospatial.org/files/?artifact_id=54838&version=1. The second trend is sharing client 'contexts'. When a user is looking into an article or a product on the web, they can easily share this information with colleagues or friends via an email that includes URLs (links to web resources) and attachments (inline data). In the case of geospatial information, a user would like to share a map created from different OGC sources, which may include for example, WMS and WFS links, and GML and KML annotations. The emerging OGC file format is called the OGC Web Services Context Document (OWS Context), which allows clients to reproduce a map previously created by someone else. Context sharing is important in a variety of domains, from emergency response, where fire, police and emergency medical personnel need to work off a common map, to multi-national military operations, where coalition forces need to share common data sources, but have cartographic displays in different languages and symbology sets. OWS Contexts can be written in XML (building upon the Atom Syndication Format) or JSON. This presentation will provide an introduction of GeoPackage and OWS Context and how they can be used to advance sharing of Earth and Space Science information.

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

PubMed Central

2011-01-01

Background Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications. Results ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms. Conclusions ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor. PMID:21548938

mzDB: A File Format Using Multiple Indexing Strategies for the Efficient Analysis of Large LC-MS/MS and SWATH-MS Data Sets*

PubMed Central

Bouyssié, David; Dubois, Marc; Nasso, Sara; Gonzalez de Peredo, Anne; Burlet-Schiltz, Odile; Aebersold, Ruedi; Monsarrat, Bernard

2015-01-01

The analysis and management of MS data, especially those generated by data independent MS acquisition, exemplified by SWATH-MS, pose significant challenges for proteomics bioinformatics. The large size and vast amount of information inherent to these data sets need to be properly structured to enable an efficient and straightforward extraction of the signals used to identify specific target peptides. Standard XML based formats are not well suited to large MS data files, for example, those generated by SWATH-MS, and compromise high-throughput data processing and storing. We developed mzDB, an efficient file format for large MS data sets. It relies on the SQLite software library and consists of a standardized and portable server-less single-file database. An optimized 3D indexing approach is adopted, where the LC-MS coordinates (retention time and m/z), along with the precursor m/z for SWATH-MS data, are used to query the database for data extraction. In comparison with XML formats, mzDB saves ∼25% of storage space and improves access times by a factor of twofold up to even 2000-fold, depending on the particular data access. Similarly, mzDB shows also slightly to significantly lower access times in comparison with other formats like mz5. Both C++ and Java implementations, converting raw or XML formats to mzDB and providing access methods, will be released under permissive license. mzDB can be easily accessed by the SQLite C library and its drivers for all major languages, and browsed with existing dedicated GUIs. The mzDB described here can boost existing mass spectrometry data analysis pipelines, offering unprecedented performance in terms of efficiency, portability, compactness, and flexibility. PMID:25505153

Satellite Level 3 & 4 Data Subsetting at NASA GES DISC

NASA Technical Reports Server (NTRS)

Huwe, Paul; Su, Jian; Loeser, Carlee; Ostrenga, Dana; Rui, Hualan; Vollmer, Bruce

2017-01-01

Earth Science data are available in many file formats (NetCDF, HDF, GRB, etc.) and in a wide range of sizes, from kilobytes to gigabytes. These properties have become a challenge to users if they are not familiar with these formats or only want a small region of interest (ROI) from a specific dataset. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we have developed and implemented a multipurpose subset service to ease user access to Earth Science data. Our Level 3 & 4 Regridder is capable of subsetting across multiple parameters (spatially, temporally, by level, and by variable) as well as having additional beneficial features (temporal means, regridding to target grids, and file conversion to other data formats). In this presentation, we will demonstrate how users can use this service to better access only the data they need in the form they require.

Satellite Level 3 & 4 Data Subsetting at NASA GES DISC

NASA Astrophysics Data System (ADS)

Huwe, P.; Su, J.; Loeser, C. F.; Ostrenga, D.; Rui, H.; Vollmer, B.

2017-12-01

Earth Science data are available in many file formats (NetCDF, HDF, GRB, etc.) and in a wide range of sizes, from kilobytes to gigabytes. These properties have become a challenge to users if they are not familiar with these formats or only want a small region of interest (ROI) from a specific dataset. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we have developed and implemented a multipurpose subset service to ease user access to Earth Science data. Our Level 3 & 4 Regridder is capable of subsetting across multiple parameters (spatially, temporally, by level, and by variable) as well as having additional beneficial features (temporal means, regridding to target grids, and file conversion to other data formats). In this presentation, we will demonstrate how users can use this service to better access only the data they need in the form they require.

Complexities in Subsetting Satellite Level 2 Data

NASA Astrophysics Data System (ADS)

Huwe, P.; Wei, J.; Albayrak, A.; Silberstein, D. S.; Alfred, J.; Savtchenko, A. K.; Johnson, J. E.; Hearty, T.; Meyer, D. J.

2017-12-01

Satellite Level 2 data presents unique challenges for tools and services. From nonlinear spatial geometry to inhomogeneous file data structure to inconsistent temporal variables to complex data variable dimensionality to multiple file formats, there are many difficulties in creating general tools for Level 2 data support. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we are implementing a general Level 2 Subsetting service for Level 2 data. In this presentation, we will unravel some of the challenges faced in creating this service and the strategies we used to surmount them.

Conjoin

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

Sjaardema, Gregory

2010-08-06

Conjoin is a code for joining sequentially in time multiple exodusII database files. It is used to create a single results or restart file from multiple results or restart files which typically arise as the result of multiple restarted analyses. The resulting output file will be the union of the input files with a status variable indicating the status of each element at the various time planes.Combining multiple exodusII files arising from a restarted analysis or combining multiple exodusII files arising from a finite element analysis with dynamic topology changes.

76 FR 43679 - Filing via the Internet; Notice of Additional File Formats for efiling

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-21

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. RM07-16-000] Filing via the Internet; Notice of Additional File Formats for efiling Take notice that the Commission has added to its list of acceptable file formats the four-character file extensions for Microsoft Office 2007/2010...

BnmrOffice: A Free Software for β-nmr Data Analysis

NASA Astrophysics Data System (ADS)

Saadaoui, Hassan

A data-analysis framework with a graphical user interface (GUI) is developed to analyze β-nmr spectra in an automated and intuitive way. This program, named BnmrOffice is written in C++ and employs the QT libraries and tools for designing the GUI, and the CERN's Minuit optimization routines for minimization. The program runs under multiple platforms, and is available for free under the terms of the GNU GPL standards. The GUI is structured in tabs to search, plot and analyze data, along other functionalities. The user can tweak the minimization options; and fit multiple data files (or runs) using single or global fitting routines with pre-defined or new models. Currently, BnmrOffice reads TRIUMF's MUD data and ASCII files, and can be extended to other formats.

Geologic map and digital database of the Romoland 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Digital preparation by Bovard, Kelly R.; Morton, Gregory

2003-01-01

Portable Document Format (.pdf) files of: This Readme; includes in Appendix I, data contained in rom_met.txt The same graphic as plotted in 2 above. Test plots have not produced precise 1:24,000- scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formationname, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above). This Readme file describes the digital data, such as types and general contents of files making up the database, and includes information on how to extract and plot the map and accompanying graphic file. Metadata information can be accessed at http://geo-nsdi.er.usgs.gov/metadata/open-file/03-102 and is included in Appendix I of this Readme.

Heads Up

MedlinePlus

... HEADS UP Resources Training Custom PDFs Mobile Apps Videos Graphics Podcasts Social Media File Formats Help: How do I view different file formats (PDF, DOC, PPT, MPEG) on this site? Adobe PDF file Microsoft PowerPoint ... file Apple Quicktime file RealPlayer file Text file ...

The SCEC Unified Community Velocity Model (UCVM) Software Framework for Distributing and Querying Seismic Velocity Models

NASA Astrophysics Data System (ADS)

Maechling, P. J.; Taborda, R.; Callaghan, S.; Shaw, J. H.; Plesch, A.; Olsen, K. B.; Jordan, T. H.; Goulet, C. A.

2017-12-01

Crustal seismic velocity models and datasets play a key role in regional three-dimensional numerical earthquake ground-motion simulation, full waveform tomography, modern physics-based probabilistic earthquake hazard analysis, as well as in other related fields including geophysics, seismology, and earthquake engineering. The standard material properties provided by a seismic velocity model are P- and S-wave velocities and density for any arbitrary point within the geographic volume for which the model is defined. Many seismic velocity models and datasets are constructed by synthesizing information from multiple sources and the resulting models are delivered to users in multiple file formats, such as text files, binary files, HDF-5 files, structured and unstructured grids, and through computer applications that allow for interactive querying of material properties. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) software framework to facilitate the registration and distribution of existing and future seismic velocity models to the SCEC community. The UCVM software framework is designed to provide a standard query interface to multiple, alternative velocity models, even if the underlying velocity models are defined in different formats or use different geographic projections. The UCVM framework provides a comprehensive set of open-source tools for querying seismic velocity model properties, combining regional 3D models and 1D background models, visualizing 3D models, and generating computational models in the form of regular grids or unstructured meshes that can be used as inputs for ground-motion simulations. The UCVM framework helps researchers compare seismic velocity models and build equivalent simulation meshes from alternative velocity models. These capabilities enable researchers to evaluate the impact of alternative velocity models in ground-motion simulations and seismic hazard analysis applications. In this poster, we summarize the key components of the UCVM framework and describe the impact it has had in various computational geoscientific applications.

Querying and Computing with BioCyc Databases

PubMed Central

Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas; Yan, Thomas; Karp, Peter D.

2006-01-01

Summary We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml PMID:15961440

Complexities in Subsetting Level 2 Data

NASA Technical Reports Server (NTRS)

Huwe, Paul; Wei, Jennifer; Meyer, David; Silberstein, David S.; Alfred, Jerome; Savtchenko, Andrey K.; Johnson, James E.; Albayrak, Arif; Hearty, Thomas

2017-01-01

Satellite Level 2 data presents unique challenges for tools and services. From nonlinear spatial geometry to inhomogeneous file data structure to inconsistent temporal variables to complex data variable dimensionality to multiple file formats, there are many difficulties in creating general tools for Level 2 data support. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we are implementing a general Level 2 Subsetting service for Level 2 data to a user-specified spatio-temporal region of interest (ROI). In this presentation, we will unravel some of the challenges faced in creating this service and the strategies we used to surmount them.

Preliminary geologic map of the Elsinore 7.5' Quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Weber, F. Harold; Digital preparation: Alvarez, Rachel M.; Burns, Diane

2003-01-01

Open-File Report 03-281 contains a digital geologic map database of the Elsinore 7.5’ quadrangle, Riverside County, California that includes: 1. ARC/INFO (Environmental Systems Research Institute, http://www.esri.com) version 7.2.1 coverages of the various elements of the geologic map. 2. A Postscript file to plot the geologic map on a topographic base, and containing a Correlation of Map Units diagram (CMU), a Description of Map Units (DMU), and an index map. 3. Portable Document Format (.pdf) files of: a. This Readme; includes in Appendix I, data contained in els_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced precise 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Documentation of a multiple-technique computer program for plotting major-ion composition of natural waters

USGS Publications Warehouse

Briel, L.I.

1993-01-01

A computer program was written to produce 6 different types of water-quality diagrams--Piper, Stiff, pie, X-Y, boxplot, and Piper 3-D--from the same file of input data. The Piper 3-D diagram is a new method that projects values from the surface of a Piper plot into a triangular prism to show how variations in chemical composition can be related to variations in other water-quality variables. This program is an analytical tool to aid in the interpretation of data. This program is interactive, and the user can select from a menu the type of diagram to be produced and a large number of individual features. Alternatively, these choices can be specified in the data file, which provides a batch mode for running the program. The program does not display water-quality diagrams directly; plots are written to a file. Four different plot- file formats are available: device-independent metafiles, Adobe PostScript graphics files, and two Hewlett-Packard graphics language formats (7475 and 7586). An ASCII data-table file is also produced to document the computed values. This program is written in Fortran '77 and uses graphics subroutines from either the PRIOR AGTK or the DISSPLA graphics library. The program has been implemented on Prime series 50 and Data General Aviion computers within the USGS; portability to other computing systems depends on the availability of the graphics library.

Conflict Detection Algorithm to Minimize Locking for MPI-IO Atomicity

NASA Astrophysics Data System (ADS)

Sehrish, Saba; Wang, Jun; Thakur, Rajeev

Many scientific applications require high-performance concurrent I/O accesses to a file by multiple processes. Those applications rely indirectly on atomic I/O capabilities in order to perform updates to structured datasets, such as those stored in HDF5 format files. Current support for atomicity in MPI-IO is provided by locking around the operations, imposing lock overhead in all situations, even though in many cases these operations are non-overlapping in the file. We propose to isolate non-overlapping accesses from overlapping ones in independent I/O cases, allowing the non-overlapping ones to proceed without imposing lock overhead. To enable this, we have implemented an efficient conflict detection algorithm in MPI-IO using MPI file views and datatypes. We show that our conflict detection scheme incurs minimal overhead on I/O operations, making it an effective mechanism for avoiding locks when they are not needed.

Chapter 21: Programmatic Interfaces - STILTS

NASA Astrophysics Data System (ADS)

Fitzpatrick, M. J.

STILTS is the Starlink Tables Infrastructure Library Tool Set developed by Mark Taylor of the former Starlink Project. STILTS is a command-line tool (see the NVOSS_HOME/bin/stilts command) providing access to the same functionality driving the TOPCAT application and can be run using either the STILTS-specific jar file, or the more general TOPCAT jar file (both are available in the NVOSS_HOME/java/lib directory and are included in the default software environment classpath). The heart of both STILTS and TOPCAT is the STIL Java library. STIL is designed to efficiently handle the input, output and processing of very large tabular datasets and the STILTS task interface makes it an ideal tool for the scripting environment. Multiple formats are supported (including FITS Binary Tables, VOTable, CSV, SQL databases and ASCII, amongst others) and while some tools will generically handle all supported formats, others are specific to the VOTable format. Converting a VOTable to a more script-friendly format is the first thing most users will encounter, but there are many other useful tools as well.

78 FR 66675 - Endangered and Threatened Wildlife; 90-Day Finding on a Petition To List Multiple Species of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-06

... to electronic comments will be accepted in Microsoft Word, Excel, or Adobe PDF file formats only... this document, identified by the code NOAA-NMFS-2013-0150, by any of the following methods: Electronic Submissions: Submit all electronic comments via the Federal eRulemaking Portal. Go to www.regulations.gov...

When Neurons Meet Electrons: Three Trends That Are Sparking Change in Computer Publishing.

ERIC Educational Resources Information Center

Cranney, Charles

1992-01-01

Three important trends in desktop publishing include (1) use of multiple media in presentation of information; (2) networking; and (3) "hot links" (integrated file-exchange formats). It is also important for college publications professionals to be familiar with sources of information about technological change and to be able to sort out the…

Adding Statistical Machine Translation Adaptation to Computer-Assisted Translation

DTIC Science & Technology

2013-09-01

are automatically searched and used to suggest possible translations; (2) spell-checkers; (3) glossaries; (4) dictionaries ; (5) alignment and...matching against TMs to propose translations; spell-checking, glossary, and dictionary look-up; support for multiple file formats; regular expressions...on Telecommunications. Tehran, 2012, 822–826. Bertoldi, N.; Federico, M. Domain Adaptation for Statistical Machine Translation with Monolingual

Autoplot: a Browser for Science Data on the Web

NASA Astrophysics Data System (ADS)

Faden, J.; Weigel, R. S.; West, E. E.; Merka, J.

2008-12-01

Autoplot (www.autoplot.org) is software for plotting data from many different sources and in many different file formats. Data from CDF, CEF, Fits, NetCDF, and OpenDAP can be plotted, along with many other sources such as ASCII tables and Excel spreadsheets. This is done by adapting these various data formats and APIs into a common data model that borrows from the netCDF and CDF data models. Autoplot uses a web browser metaphor to simplify use. The user specifies a parameter URL, for example a CDF file accessible via http with a parameter name appended, and the file resource is downloaded and the parameter is rendered in a scientifically meaningful way. When data span multiple files, the user can use a file name template in the URL to aggregate (combine) a set of remote files. So the problem of aggregating data across file boundaries is handled on the client side, allowing simple web servers to be used. The das2 graphics library provides rich controls for exploring the data. Scripting is supported through Python, providing not just programmatic control, but for calculating new parameters in a language that will look familiar to IDL and Matlab users. Autoplot is Java-based software, and will run on most computers without a burdensome installation process. It can also used as an applet or as a servlet that serves static images. Autoplot was developed as part of the Virtual Radiation Belt Observatory (ViRBO) project, and is also being used for the Virtual Magnetospheric Observatory (VMO). It is expected that this flexible, general-purpose plotting tool will be useful for allowing a data provider to add instant visualization capabilities to a directory of files or for general use in the Virtual Observatory environment.

Interoperability format translation and transformation between IFC architectural design file and simulation file formats

DOEpatents

Chao, Tian-Jy; Kim, Younghun

2015-02-03

Automatically translating a building architecture file format (Industry Foundation Class) to a simulation file, in one aspect, may extract data and metadata used by a target simulation tool from a building architecture file. Interoperability data objects may be created and the extracted data is stored in the interoperability data objects. A model translation procedure may be prepared to identify a mapping from a Model View Definition to a translation and transformation function. The extracted data may be transformed using the data stored in the interoperability data objects, an input Model View Definition template, and the translation and transformation function to convert the extracted data to correct geometric values needed for a target simulation file format used by the target simulation tool. The simulation file in the target simulation file format may be generated.

Rapid Generation of Large Dimension Photon Sieve Designs

NASA Technical Reports Server (NTRS)

Hariharan, Shravan; Fitzpatrick, Sean; Kim, Hyun Jung; Julian, Matthew; Sun, Wenbo; Tedjojuwono, Ken; MacDonnell, David

2017-01-01

A photon sieve is a revolutionary optical instrument that provides high resolution imaging at a fraction of the weight of typical telescopes (areal density of 0.3 kg/m2 compared to 25 kg/m2 for the James Webb Space Telescope). The photon sieve is a variation of a Fresnel Zone Plate consisting of many small holes spread out in a ring-like pattern, which focuses light of a specific wavelength by diffraction. The team at NASA Langley Research Center has produced a variety of small photon sieves for testing. However, it is necessary to increase both the scale and rate of production, as a single sieve previously took multiple weeks to design and fabricate. This report details the different methods used in producing photon sieve designs in two file formats: CIF and DXF. The difference between these methods, and the two file formats were compared, to determine the most efficient design process. Finally, a step-by-step sieve design and fabrication process was described. The design files can be generated in both formats using an editing tool such as Microsoft Excel. However, an approach using a MATLAB program reduced the computing time of the designs and increased the ability of the user to generate large photon sieve designs. Although the CIF generation process was deemed the most efficient, the design techniques for both file types have been proven to generate complete photon sieves that can be used for scientific applications

The Open Spectral Database: an open platform for sharing and searching spectral data.

PubMed

Chalk, Stuart J

2016-01-01

A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

Interoperability format translation and transformation between IFC architectural design file and simulation file formats

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

Chao, Tian-Jy; Kim, Younghun

Automatically translating a building architecture file format (Industry Foundation Class) to a simulation file, in one aspect, may extract data and metadata used by a target simulation tool from a building architecture file. Interoperability data objects may be created and the extracted data is stored in the interoperability data objects. A model translation procedure may be prepared to identify a mapping from a Model View Definition to a translation and transformation function. The extracted data may be transformed using the data stored in the interoperability data objects, an input Model View Definition template, and the translation and transformation function tomore » convert the extracted data to correct geometric values needed for a target simulation file format used by the target simulation tool. The simulation file in the target simulation file format may be generated.« less

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

Temple, Brian Allen; Armstrong, Jerawan Chudoung

This document is a mid-year report on a deliverable for the PYTHON Radiography Analysis Tool (PyRAT) for project LANL12-RS-107J in FY15. The deliverable is deliverable number 2 in the work package and is titled “Add the ability to read in more types of image file formats in PyRAT”. Right now PyRAT can only read in uncompressed TIF files (tiff files). It is planned to expand the file formats that can be read by PyRAT, making it easier to use in more situations. A summary of the file formats added include jpeg, jpg, png and formatted ASCII files.

Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing.

PubMed

Tikkanen, Tuomas; Leroy, Bernard; Fournier, Jean Louis; Risques, Rosa Ana; Malcikova, Jitka; Soussi, Thierry

2018-07-01

Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/. © 2018 Wiley Periodicals, Inc.

Data files from the Grays Harbor Sediment Transport Experiment Spring 2001

USGS Publications Warehouse

Landerman, Laura A.; Sherwood, Christopher R.; Gelfenbaum, Guy; Lacy, Jessica; Ruggiero, Peter; Wilson, Douglas; Chisholm, Tom; Kurrus, Keith

2005-01-01

This publication consists of two DVD-ROMs, both of which are presented here. This report describes data collected during the Spring 2001 Grays Harbor Sediment Transport Experiment, and provides additional information needed to interpret the data. Two DVDs accompany this report; both contain documentation in html format that assist the user in navigating through the data. DVD-ROM-1 contains a digital version of this report in .pdf format, raw Aquatec acoustic backscatter (ABS) data in .zip format, Sonar data files in .avi format, and coastal processes and morphology data in ASCII format. ASCII data files are provided in .zip format; bundled coastal processes ASCII files are separated by deployment and instrument; bundled morphology ASCII files are separated into monthly data collection efforts containing the beach profiles collected (or extracted from the surface map) at that time; weekly surface maps are also bundled together. DVD-ROM-2 contains a digital version of this report in .pdf format, the binary data files collected by the SonTek instrumentation, calibration files for the pressure sensors, and Matlab m-files for loading the ABS data into Matlab and cleaning-up the optical backscatter (OBS) burst time-series data.

File format for normalizing radiological concentration exposure rate and dose rate data for the effects of radioactive decay and weathering processes

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

Kraus, Terrence D.

2017-04-01

This report specifies the electronic file format that was agreed upon to be used as the file format for normalized radiological data produced by the software tool developed under this TI project. The NA-84 Technology Integration (TI) Program project (SNL17-CM-635, Normalizing Radiological Data for Analysis and Integration into Models) investigators held a teleconference on December 7, 2017 to discuss the tasks to be completed under the TI program project. During this teleconference, the TI project investigators determined that the comma-separated values (CSV) file format is the most suitable file format for the normalized radiological data that will be outputted frommore » the normalizing tool developed under this TI project. The CSV file format was selected because it provides the requisite flexibility to manage different types of radiological data (i.e., activity concentration, exposure rate, dose rate) from other sources [e.g., Radiological Assessment and Monitoring System (RAMS), Aerial Measuring System (AMS), Monitoring and Sampling). The CSV file format also is suitable for the file format of the normalized radiological data because this normalized data can then be ingested by other software [e.g., RAMS, Visual Sampling Plan (VSP)] used by the NA-84’s Consequence Management Program.« less

Proposed color workflow solution from mobile and website to printing

NASA Astrophysics Data System (ADS)

Qiao, Mu; Wyse, Terry

2015-03-01

With the recent introduction of mobile devices and development in client side application technologies, there is an explosion of the parameter matrix for color management: hardware platform (computer vs. mobile), operating system (Windows, Mac OS, Android, iOS), client application (Flesh, IE, Firefox, Safari, Chrome), and file format (JPEG, TIFF, PDF of various versions). In a modern digital print shop, multiple print solutions are used: digital presses, wide format inkjet, dye sublimation inkjet are used to produce a wide variety of customizable products from photo book, personalized greeting card, canvas, mobile phone case and more. In this paper, we outline a strategy spans from client side application, print file construction, to color setup on printer to manage consistency and also achieve what-you-see-is-what-you-get for customers who are using a wide variety of technologies in viewing and ordering product.

77 FR 59692 - 2014 Diversity Immigrant Visa Program

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... the E-DV system. The entry will not be accepted and must be resubmitted. Group or family photographs... must be in the Joint Photographic Experts Group (JPEG) format. Image File Size: The maximum file size...). Image File Format: The image must be in the Joint Photographic Experts Group (JPEG) format. Image File...

Data Fusion and Visualization with the OpenEarth Framework (OEF)

NASA Astrophysics Data System (ADS)

Nadeau, D. R.; Baru, C.; Fouch, M. J.; Crosby, C. J.

2010-12-01

Data fusion is an increasingly important problem to solve as we strive to integrate data from multiple sources and build better models of the complex processes operating at the Earth’s surface and its interior. These data are often large, multi-dimensional, and subject to differing conventions for file formats, data structures, coordinate spaces, units of measure, and metadata organization. When visualized, these data require differing, and often conflicting, conventions for visual representations, dimensionality, icons, color schemes, labeling, and interaction. These issues make the visualization of fused Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data fusion and visualization suite of software being developed at the Supercomputer Center at the University of California, San Diego. Funded by the NSF, the project is leveraging virtual globe technology from NASA’s WorldWind to create interactive 3D visualization tools that combine layered data from a variety of sources to create a holistic view of features at, above, and beneath the Earth’s surface. The OEF architecture is cross-platform, multi-threaded, modular, and based upon Java. The OEF’s modular approach yields a collection of compatible mix-and-match components for assembling custom applications. Available modules support file format handling, web service communications, data management, data filtering, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats. Each one imports data into a general-purpose data representation that supports multidimensional grids, topography, points, lines, polygons, images, and more. From there these data then may be manipulated, merged, filtered, reprojected, and visualized. Visualization features support conventional and new visualization techniques for looking at topography, tomography, maps, and feature geometry. 3D grid data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery along with data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers and a common 3D+time coordinate space. Data management within the OEF handles and hides the quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Derived data are computed automatically to support interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization is accelerated by 3D graphics hardware found on today’s computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

User's Manual for Aerofcn: a FORTRAN Program to Compute Aerodynamic Parameters

NASA Technical Reports Server (NTRS)

Conley, Joseph L.

1992-01-01

The computer program AeroFcn is discussed. AeroFcn is a utility program that computes the following aerodynamic parameters: geopotential altitude, Mach number, true velocity, dynamic pressure, calibrated airspeed, equivalent airspeed, impact pressure, total pressure, total temperature, Reynolds number, speed of sound, static density, static pressure, static temperature, coefficient of dynamic viscosity, kinematic viscosity, geometric altitude, and specific energy for a standard- or a modified standard-day atmosphere using compressible flow and normal shock relations. Any two parameters that define a unique flight condition are selected, and their values are entered interactively. The remaining parameters are computed, and the solutions are stored in an output file. Multiple cases can be run, and the multiple case solutions can be stored in another output file for plotting. Parameter units, the output format, and primary constants in the atmospheric and aerodynamic equations can also be changed.

NAVAIR Portable Source Initiative (NPSI) Standard for Reusable Source Dataset Metadata (RSDM) V2.4

DTIC Science & Technology

2012-09-26

defining a raster file format: <RasterFileFormat> <FormatName>TIFF</FormatName> <Order>BIP</Order> < DataType >8-BIT_UNSIGNED</ DataType ...interleaved by line (BIL); Band interleaved by pixel (BIP). element RasterFileFormatType/ DataType diagram type restriction of xsd:string facets

An Efficient Format for Nearly Constant-Time Access to Arbitrary Time Intervals in Large Trace Files

DOE PAGES

Chan, Anthony; Gropp, William; Lusk, Ewing

2008-01-01

A powerful method to aid in understanding the performance of parallel applications uses log or trace files containing time-stamped events and states (pairs of events). These trace files can be very large, often hundreds or even thousands of megabytes. Because of the cost of accessing and displaying such files, other methods are often used that reduce the size of the tracefiles at the cost of sacrificing detail or other information. This paper describes a hierarchical trace file format that provides for display of an arbitrary time window in a time independent of the total size of the file and roughlymore » proportional to the number of events within the time window. This format eliminates the need to sacrifice data to achieve a smaller trace file size (since storage is inexpensive, it is necessary only to make efficient use of bandwidth to that storage). The format can be used to organize a trace file or to create a separate file of annotations that may be used with conventional trace files. We present an analysis of the time to access all of the events relevant to an interval of time and we describe experiments demonstrating the performance of this file format.« less

Isostatic gravity map and principal facts for 694 gravity stations in Yellowstone National Park and vicinity, Wyoming, Montana, and Idaho

USGS Publications Warehouse

Carle, S.F.; Glen, J.M.; Langenheim, V.E.; Smith, R.B.; Oliver, H.W.

1990-01-01

The report presents the principal facts for gravity stations compiled for Yellowstone National Park and vicinity. The gravity data were compiled from three sources: Defense Mapping Agency, University of Utah, and U.S. Geological Survey. Part A of the report is a paper copy describing how the compilation was done and presenting the data in tabular format as well as a map; part B is a 5-1/4 inch floppy diskette containing only the data files in ASCII format. Requirements for part B: IBM PC or compatible, DOS v. 2.0 or higher. Files contained on this diskette: DOD.ISO -- File containing the principal facts of the 514 gravity stations obtained from the Defense Mapping Agency. The data are in Plouff format* (see file PFTAB.TEX). UTAH.ISO -- File containing the principal facts of 153 gravity stations obtained from the University of Utah. Data are in Plouff format. USGS.ISO -- File containing the principal facts of 27 gravity stations collected by the U.S. Geological Survey in July 1987. Data are in Plouff format. PFTAB.TXT -- File containing explanation of principal fact format. ACC.TXT -- File containing explanation of accuracy codes.

CFL3D User's Manual (Version 5.0)

NASA Technical Reports Server (NTRS)

Krist, Sherrie L.; Biedron, Robert T.; Rumsey, Christopher L.

1998-01-01

This document is the User's Manual for the CFL3D computer code, a thin-layer Reynolds-averaged Navier-Stokes flow solver for structured multiple-zone grids. Descriptions of the code's input parameters, non-dimensionalizations, file formats, boundary conditions, and equations are included. Sample 2-D and 3-D test cases are also described, and many helpful hints for using the code are provided.

TiConverter: A training image converting tool for multiple-point geostatistics

NASA Astrophysics Data System (ADS)

Fadlelmula F., Mohamed M.; Killough, John; Fraim, Michael

2016-11-01

TiConverter is a tool developed to ease the application of multiple-point geostatistics whether by the open source Stanford Geostatistical Modeling Software (SGeMS) or other available commercial software. TiConverter has a user-friendly interface and it allows the conversion of 2D training images into numerical representations in four different file formats without the need for additional code writing. These are the ASCII (.txt), the geostatistical software library (GSLIB) (.txt), the Isatis (.dat), and the VTK formats. It performs the conversion based on the RGB color system. In addition, TiConverter offers several useful tools including image resizing, smoothing, and segmenting tools. The purpose of this study is to introduce the TiConverter, and to demonstrate its application and advantages with several examples from the literature.

AgMIP Training in Multiple Crop Models and Tools

NASA Technical Reports Server (NTRS)

Boote, Kenneth J.; Porter, Cheryl H.; Hargreaves, John; Hoogenboom, Gerrit; Thornburn, Peter; Mutter, Carolyn

2015-01-01

The Agricultural Model Intercomparison and Improvement Project (AgMIP) has the goal of using multiple crop models to evaluate climate impacts on agricultural production and food security in developed and developing countries. There are several major limitations that must be overcome to achieve this goal, including the need to train AgMIP regional research team (RRT) crop modelers to use models other than the ones they are currently familiar with, plus the need to harmonize and interconvert the disparate input file formats used for the various models. Two activities were followed to address these shortcomings among AgMIP RRTs to enable them to use multiple models to evaluate climate impacts on crop production and food security. We designed and conducted courses in which participants trained on two different sets of crop models, with emphasis on the model of least experience. In a second activity, the AgMIP IT group created templates for inputting data on soils, management, weather, and crops into AgMIP harmonized databases, and developed translation tools for converting the harmonized data into files that are ready for multiple crop model simulations. The strategies for creating and conducting the multi-model course and developing entry and translation tools are reviewed in this chapter.

Mapping DICOM to OpenDocument format

NASA Astrophysics Data System (ADS)

Yu, Cong; Yao, Zhihong

2009-02-01

In order to enhance the readability, extensibility and sharing of DICOM files, we have introduced XML into DICOM file system (SPIE Volume 5748)[1] and the multilayer tree structure into DICOM (SPIE Volume 6145)[2]. In this paper, we proposed mapping DICOM to ODF(OpenDocument Format), for it is also based on XML. As a result, the new format realizes the separation of content(including text content and image) and display style. Meanwhile, since OpenDocument files take the format of a ZIP compressed archive, the new kind of DICOM files can benefit from ZIP's lossless compression to reduce file size. Moreover, this open format can also guarantee long-term access to data without legal or technical barriers, making medical images accessible to various fields.

18 CFR 50.3 - Applications/pre-filing; rules and format.

Code of Federal Regulations, 2010 CFR

2010-04-01

... filings must be signed in compliance with § 385.2005 of this chapter. (e) The Commission will conduct a... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Applications/pre-filing... INTERSTATE ELECTRIC TRANSMISSION FACILITIES § 50.3 Applications/pre-filing; rules and format. (a) Filings are...

Manual for Getdata Version 3.1: a FORTRAN Utility Program for Time History Data

NASA Technical Reports Server (NTRS)

Maine, Richard E.

1987-01-01

This report documents version 3.1 of the GetData computer program. GetData is a utility program for manipulating files of time history data, i.e., data giving the values of parameters as functions of time. The most fundamental capability of GetData is extracting selected signals and time segments from an input file and writing the selected data to an output file. Other capabilities include converting file formats, merging data from several input files, time skewing, interpolating to common output times, and generating calculated output signals as functions of the input signals. This report also documents the interface standards for the subroutines used by GetData to read and write the time history files. All interface to the data files is through these subroutines, keeping the main body of GetData independent of the precise details of the file formats. Different file formats can be supported by changes restricted to these subroutines. Other computer programs conforming to the interface standards can call the same subroutines to read and write files in compatible formats.

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.

Arkansas and Louisiana Aeromagnetic and Gravity Maps and Data - A Website for Distribution of Data

USGS Publications Warehouse

Bankey, Viki; Daniels, David L.

2008-01-01

This report contains digital data, image files, and text files describing data formats for aeromagnetic and gravity data used to compile the State aeromagnetic and gravity maps of Arkansas and Louisiana. The digital files include grids, images, ArcInfo, and Geosoft compatible files. In some of the data folders, ASCII files with the extension 'txt' describe the format and contents of the data files. Read the 'txt' files before using the data files.

PLOT3D user's manual

NASA Technical Reports Server (NTRS)

Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

1990-01-01

PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

Mass spectrometer output file format mzML.

PubMed

Deutsch, Eric W

2010-01-01

Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provides clear terms and definitions for the spectral metadata, and a semantic validation rules mapping file allows the mzML semantic validator to insure that an mzML document complies with one of several levels of requirements. Complete documentation and example files insure that the format may be uniformly implemented. At the time of release, there already existed several implementations of the format and vendors have committed to supporting the format in their products.

ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

PubMed

Hoffmann, Nils; Stoye, Jens

2009-08-15

We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.

An easy and effective approach to manage radiologic portable document format (PDF) files using iTunes.

PubMed

Qian, Li Jun; Zhou, Mi; Xu, Jian Rong

2008-07-01

The objective of this article is to explain an easy and effective approach for managing radiologic files in portable document format (PDF) using iTunes. PDF files are widely used as a standard file format for electronic publications as well as for medical online documents. Unfortunately, there is a lack of powerful software to manage numerous PDF documents. In this article, we explain how to use the hidden function of iTunes (Apple Computer) to manage PDF documents as easily as managing music files.

NetCDF4/HDF5 and Linked Data in the Real World - Enriching Geoscientific Metadata without Bloat

NASA Astrophysics Data System (ADS)

Ip, Alex; Car, Nicholas; Druken, Kelsey; Poudjom-Djomani, Yvette; Butcher, Stirling; Evans, Ben; Wyborn, Lesley

2017-04-01

NetCDF4 has become the dominant generic format for many forms of geoscientific data, leveraging (and constraining) the versatile HDF5 container format, while providing metadata conventions for interoperability. However, the encapsulation of detailed metadata within each file can lead to metadata "bloat", and difficulty in maintaining consistency where metadata is replicated to multiple locations. Complex conceptual relationships are also difficult to represent in simple key-value netCDF metadata. Linked Data provides a practical mechanism to address these issues by associating the netCDF files and their internal variables with complex metadata stored in Semantic Web vocabularies and ontologies, while complying with and complementing existing metadata conventions. One of the stated objectives of the netCDF4/HDF5 formats is that they should be self-describing: containing metadata sufficient for cataloguing and using the data. However, this objective can be regarded as only partially-met where details of conventions and definitions are maintained externally to the data files. For example, one of the most widely used netCDF community standards, the Climate and Forecasting (CF) Metadata Convention, maintains standard vocabularies for a broad range of disciplines across the geosciences, but this metadata is currently neither readily discoverable nor machine-readable. We have previously implemented useful Linked Data and netCDF tooling (ncskos) that associates netCDF files, and individual variables within those files, with concepts in vocabularies formulated using the Simple Knowledge Organization System (SKOS) ontology. NetCDF files contain Uniform Resource Identifier (URI) links to terms represented as SKOS Concepts, rather than plain-text representations of those terms, so we can use simple, standardised web queries to collect and use rich metadata for the terms from any Linked Data-presented SKOS vocabulary. Geoscience Australia (GA) manages a large volume of diverse geoscientific data, much of which is being translated from proprietary formats to netCDF at NCI Australia. This data is made available through the NCI National Environmental Research Data Interoperability Platform (NERDIP) for programmatic access and interdisciplinary analysis. The netCDF files contain both scientific data variables (e.g. gravity, magnetic or radiometric values), but also domain-specific operational values (e.g. specific instrument parameters) best described fully in formal vocabularies. Our ncskos codebase provides access to multiple stores of detailed external metadata in a standardised fashion. Geophysical datasets are generated from a "survey" event, and GA maintains corporate databases of all surveys and their associated metadata. It is impractical to replicate the full source survey metadata into each netCDF dataset so, instead, we link the netCDF files to survey metadata using public Linked Data URIs. These URIs link to Survey class objects which we model as a subclass of Activity objects as defined by the PROV Ontology, and we provide URI resolution for them via a custom Linked Data API which draws current survey metadata from GA's in-house databases. We have demonstrated that Linked Data is a practical way to associate netCDF data with detailed, external metadata. This allows us to ensure that catalogued metadata is kept consistent with metadata points-of-truth, and we can infer complex conceptual relationships not possible with netCDF key-value attributes alone.

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

Keszei, András P; Berkels, Benjamin; Deserno, Thomas M

2017-02-01

We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.

76 FR 10045 - Notice of Proposed Information Collection: Comment Request; “eLogic Model” Grant Performance...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

... recommends not more than 32 characters). DO NOT convert Word files or Excel files into PDF format. Converting... not allow HUD to enter data from the Excel files into a database. DO NOT save your logic model in .xlsm format. If necessary save as an Excel 97-2003 .xls format. Using the .xlsm format can result in a...

Geologic map of the Corona South 7.5' quadrangle, Riverside and Orange counties, California

USGS Publications Warehouse

Gray, C.H.; Morton, Douglas M.; Weber, F. Harold; Digital preparation by Bovard, Kelly R.; O'Brien, Timothy

2002-01-01

a. A Readme file; includes in Appendix I, data contained in crs_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

12 CFR 335.801 - Inapplicable SEC regulations; FDIC substituted regulations; additional information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... a continuing hardship exemption under these rules may file the forms with the FDIC in paper format... these rules may file the appropriate forms with the FDIC in paper format. Instructions for continuing...) Previously filed exhibits, whether in paper or electronic format, may be incorporated by reference into an...

12 CFR 335.801 - Inapplicable SEC regulations; FDIC substituted regulations; additional information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... a continuing hardship exemption under these rules may file the forms with the FDIC in paper format... these rules may file the appropriate forms with the FDIC in paper format. Instructions for continuing...) Previously filed exhibits, whether in paper or electronic format, may be incorporated by reference into an...

12 CFR 335.801 - Inapplicable SEC regulations; FDIC substituted regulations; additional information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... a continuing hardship exemption under these rules may file the forms with the FDIC in paper format... these rules may file the appropriate forms with the FDIC in paper format. Instructions for continuing...) Previously filed exhibits, whether in paper or electronic format, may be incorporated by reference into an...

12 CFR 335.801 - Inapplicable SEC regulations; FDIC substituted regulations; additional information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... a continuing hardship exemption under these rules may file the forms with the FDIC in paper format... these rules may file the appropriate forms with the FDIC in paper format. Instructions for continuing...) Previously filed exhibits, whether in paper or electronic format, may be incorporated by reference into an...

A Web Portal-Based Time-Aware KML Animation Tool for Exploring Spatiotemporal Dynamics of Hydrological Events

NASA Astrophysics Data System (ADS)

Bao, X.; Cai, X.; Liu, Y.

2009-12-01

Understanding spatiotemporal dynamics of hydrological events such as storms and droughts is highly valuable for decision making on disaster mitigation and recovery. Virtual Globe-based technologies such as Google Earth and Open Geospatial Consortium KML standards show great promises for collaborative exploration of such events using visual analytical approaches. However, currently there are two barriers for wider usage of such approaches. First, there lacks an easy way to use open source tools to convert legacy or existing data formats such as shapefiles, geotiff, or web services-based data sources to KML and to produce time-aware KML files. Second, an integrated web portal-based time-aware animation tool is currently not available. Thus users usually share their files in the portal but have no means to visually explore them without leaving the portal environment which the users are familiar with. We develop a web portal-based time-aware KML animation tool for viewing extreme hydrologic events. The tool is based on Google Earth JavaScript API and Java Portlet standard 2.0 JSR-286, and it is currently deployable in one of the most popular open source portal frameworks, namely Liferay. We have also developed an open source toolkit kml-soc-ncsa (http://code.google.com/p/kml-soc-ncsa/) to facilitate the conversion of multiple formats into KML and the creation of time-aware KML files. We illustrate our tool using some example cases, in which drought and storm events with both time and space dimension can be explored in this web-based KML animation portlet. The tool provides an easy-to-use web browser-based portal environment for multiple users to collaboratively share and explore their time-aware KML files as well as improving the understanding of the spatiotemporal dynamics of the hydrological events.

Transferable Output ASCII Data (TOAD) gateway: Version 1.0 user's guide

NASA Technical Reports Server (NTRS)

Bingel, Bradford D.

1991-01-01

The Transferable Output ASCII Data (TOAD) Gateway, release 1.0 is described. This is a software tool for converting tabular data from one format into another via the TOAD format. This initial release of the Gateway allows free data interchange among the following file formats: TOAD; Standard Interface File (SIF); Program to Optimize Simulated Trajectories (POST) input; Comma Separated Value (TSV); and a general free-form file format. As required, additional formats can be accommodated quickly and easily.

Sensitivity Data File Formats

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

Rearden, Bradley T.

2016-04-01

The format of the TSUNAMI-A sensitivity data file produced by SAMS for cases with deterministic transport solutions is given in Table 6.3.A.1. The occurrence of each entry in the data file is followed by an identification of the data contained on each line of the file and the FORTRAN edit descriptor denoting the format of each line. A brief description of each line is also presented. A sample of the TSUNAMI-A data file for the Flattop-25 sample problem is provided in Figure 6.3.A.1. Here, only two profiles out of the 130 computed are shown.

TOAD Editor

NASA Technical Reports Server (NTRS)

Bingle, Bradford D.; Shea, Anne L.; Hofler, Alicia S.

1993-01-01

Transferable Output ASCII Data (TOAD) computer program (LAR-13755), implements format designed to facilitate transfer of data across communication networks and dissimilar host computer systems. Any data file conforming to TOAD format standard called TOAD file. TOAD Editor is interactive software tool for manipulating contents of TOAD files. Commonly used to extract filtered subsets of data for visualization of results of computation. Also offers such user-oriented features as on-line help, clear English error messages, startup file, macroinstructions defined by user, command history, user variables, UNDO features, and full complement of mathematical statistical, and conversion functions. Companion program, TOAD Gateway (LAR-14484), converts data files from variety of other file formats to that of TOAD. TOAD Editor written in FORTRAN 77.

78 FR 17233 - Notice of Opportunity To File Amicus Briefs

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-20

.... Any commonly-used word processing format or PDF format is acceptable; text formats are preferable to image formats. Briefs may also be filed with the Office of the Clerk of the Board, Merit Systems...

An OpenEarth Framework (OEF) for Integrating and Visualizing Earth Science Data

NASA Astrophysics Data System (ADS)

Moreland, J. L.; Nadeau, D. R.; Baru, C.; Crosby, C. J.

2009-12-01

The integration of data is essential to make transformative progress in understanding the complex processes operating at the Earth’s surface and within its interior. While our current ability to collect massive amounts of data, develop structural models, and generate high-resolution dynamics models is well developed, our ability to quantitatively integrate these data and models into holistic interpretations of Earth systems is poorly developed. We lack the basic tools to realize a first-order goal in Earth science of developing integrated 4D models of Earth structure and processes using a complete range of available constraints, at a time when the research agenda of major efforts such as EarthScope demand such a capability. Among the challenges to 3D data integration are data that may be in different coordinate spaces, units, value ranges, file formats, and data structures. While several file format standards exist, they are infrequently or incorrectly used. Metadata is often missing, misleading, or relegated to README text files along side the data. This leaves much of the work to integrate data bogged down by simple data management tasks. The OpenEarth Framework (OEF) being developed by GEON addresses these data management difficulties. The software incorporates file format parsers, data interpretation heuristics, user interfaces to prompt for missing information, and visualization techniques to merge data into a common visual model. The OEF’s data access libraries parse formal and de facto standard file formats and map their data into a common data model. The software handles file format quirks, storage details, caching, local and remote file access, and web service protocol handling. Heuristics are used to determine coordinate spaces, units, and other key data features. Where multiple data structure, naming, and file organization conventions exist, those heuristics check for each convention’s use to find a high confidence interpretation of the data. When no convention or embedded data yields a suitable answer, the user is prompted to fill in the blanks. The OEF’s interaction libraries assist in the construction of user interfaces for data management. These libraries support data import, data prompting, data introspection, the management of the contents of a common data model, and the creation of derived data to support visualization. Finally, visualization libraries provide interactive visualization using an extended version of NASA WorldWind. The OEF viewer supports visualization of terrains, point clouds, 3D volumes, imagery, cutting planes, isosurfaces, and more. Data may be color coded, shaded, and displayed above, or below the terrain, and always registered into a common coordinate space. The OEF architecture is open and cross-platform software libraries are available separately for use with other software projects, while modules from other projects may be integrated into the OEF to extend its features. The OEF is currently being used to visualize data from EarthScope-related research in the Western US.

Video multiple watermarking technique based on image interlacing using DWT.

PubMed

Ibrahim, Mohamed M; Abdel Kader, Neamat S; Zorkany, M

2014-01-01

Digital watermarking is one of the important techniques to secure digital media files in the domains of data authentication and copyright protection. In the nonblind watermarking systems, the need of the original host file in the watermark recovery operation makes an overhead over the system resources, doubles memory capacity, and doubles communications bandwidth. In this paper, a robust video multiple watermarking technique is proposed to solve this problem. This technique is based on image interlacing. In this technique, three-level discrete wavelet transform (DWT) is used as a watermark embedding/extracting domain, Arnold transform is used as a watermark encryption/decryption method, and different types of media (gray image, color image, and video) are used as watermarks. The robustness of this technique is tested by applying different types of attacks such as: geometric, noising, format-compression, and image-processing attacks. The simulation results show the effectiveness and good performance of the proposed technique in saving system resources, memory capacity, and communications bandwidth.

Displaying Composite and Archived Soundings in the Advanced Weather Interactive Processing System

NASA Technical Reports Server (NTRS)

Barrett, Joe H., III; Volkmer, Matthew R.; Blottman, Peter F.; Sharp, David W.

2008-01-01

In a previous task, the Applied Meteorology Unit (AMU) developed spatial and temporal climatologies of lightning occurrence based on eight atmospheric flow regimes. The AMU created climatological, or composite, soundings of wind speed and direction, temperature, and dew point temperature at four rawinsonde observation stations at Jacksonville, Tampa, Miami, and Cape Canaveral Air Force Station, for each of the eight flow regimes. The composite soundings were delivered to the National Weather Service (NWS) Melbourne (MLB) office for display using the National version of the Skew-T Hodograph analysis and Research Program (NSHARP) software program. The NWS MLB requested the AMU make the composite soundings available for display in the Advanced Weather Interactive Processing System (AWIPS), so they could be overlaid on current observed soundings. This will allow the forecasters to compare the current state of the atmosphere with climatology. This presentation describes how the AMU converted the composite soundings from NSHARP Archive format to Network Common Data Form (NetCDF) format, so that the soundings could be displayed in AWl PS. The NetCDF is a set of data formats, programming interfaces, and software libraries used to read and write scientific data files. In AWIPS, each meteorological data type, such as soundings or surface observations, has a unique NetCDF format. Each format is described by a NetCDF template file. Although NetCDF files are in binary format, they can be converted to a text format called network Common data form Description Language (CDL). A software utility called ncgen is used to create a NetCDF file from a CDL file, while the ncdump utility is used to create a CDL file from a NetCDF file. An AWIPS receives soundings in Binary Universal Form for the Representation of Meteorological data (BUFR) format (http://dss.ucar.edu/docs/formats/bufr/), and then decodes them into NetCDF format. Only two sounding files are generated in AWIPS per day. One file contains all of the soundings received worldwide between 0000 UTC and 1200 UTC, and the other includes all soundings between 1200 UTC and 0000 UTC. In order to add the composite soundings into AWIPS, a procedure was created to configure, or localize, AWIPS. This involved modifying and creating several configuration text files. A unique fourcharacter site identifier was created for each of the 32 soundings so each could be viewed separately. The first three characters were based on the site identifier of the observed sounding, while the last character was based on the flow regime. While researching the localization process for soundings, the AMU discovered a method of archiving soundings so old soundings would not get purged automatically by AWl PS. This method could provide an alternative way of localizing AWl PS for composite soundings. In addition, this would allow forecasters to use archived soundings in AWIPS for case studies. A test sounding file in NetCDF format was written in order to verify the correct format for soundings in AWIPS. After the file was viewed successfully in AWIPS, the AMU wrote a software program in the Tool Command Language/Tool Kit (Tcl/Tk) language to convert the 32 composite soundings from NSHARP Archive to CDL format. The ncgen utility was then used to convert the CDL file to a NetCDF file. The NetCDF file could then be read and displayed in AWIPS.

Tools for Requirements Management: A Comparison of Telelogic DOORS and the HiVe

DTIC Science & Technology

2006-07-01

types DOORS deals with are text files, spreadsheets, FrameMaker , rich text, Microsoft Word and Microsoft Project. 2.5.1 Predefined file formats DOORS...during the export. DOORS exports FrameMaker files in an incomplete format, meaning DOORS exported files will have to be opened in FrameMaker and saved

76 FR 10405 - Federal Copyright Protection of Sound Recordings Fixed Before February 15, 1972

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-24

... file in either the Adobe Portable Document File (PDF) format that contains searchable, accessible text (not an image); Microsoft Word; WordPerfect; Rich Text Format (RTF); or ASCII text file format (not a..., comments may be delivered in hard copy. If hand delivered by a private party, an original [[Page 10406...

The prevalence of encoded digital trace evidence in the nonfile space of computer media(,) (.).

PubMed

Garfinkel, Simson L

2014-09-01

Forensically significant digital trace evidence that is frequently present in sectors of digital media not associated with allocated or deleted files. Modern digital forensic tools generally do not decompress such data unless a specific file with a recognized file type is first identified, potentially resulting in missed evidence. Email addresses are encoded differently for different file formats. As a result, trace evidence can be categorized as Plain in File (PF), Encoded in File (EF), Plain Not in File (PNF), or Encoded Not in File (ENF). The tool bulk_extractor finds all of these formats, but other forensic tools do not. A study of 961 storage devices purchased on the secondary market and shows that 474 contained encoded email addresses that were not in files (ENF). Different encoding formats are the result of different application programs that processed different kinds of digital trace evidence. Specific encoding formats explored include BASE64, GZIP, PDF, HIBER, and ZIP. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Journal of Forensic Sciences published by Wiley Periodicals, Inc. on behalf of American Academy of Forensic Sciences.

Highway Safety Information System guidebook for the Minnesota state data files. Volume 1 : SAS file formats

DOT National Transportation Integrated Search

2001-02-01

The Minnesota data system includes the following basic files: Accident data (Accident File, Vehicle File, Occupant File); Roadlog File; Reference Post File; Traffic File; Intersection File; Bridge (Structures) File; and RR Grade Crossing File. For ea...

PDB explorer -- a web based algorithm for protein annotation viewer and 3D visualization.

PubMed

Nayarisseri, Anuraj; Shardiwal, Rakesh Kumar; Yadav, Mukesh; Kanungo, Neha; Singh, Pooja; Shah, Pratik; Ahmed, Sheaza

2014-12-01

The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which therefore can be described in the PDB format and have been deposited in PDB database. PDB is a machine generated file, it's not human readable format, to read this file we need any computational tool to understand it. The objective of our present study is to develop a free online software for retrieval, visualization and reading of annotation of a protein 3D structure which is available in PDB database. Main aim is to create PDB file in human readable format, i.e., the information in PDB file is converted in readable sentences. It displays all possible information from a PDB file including 3D structure of that file. Programming languages and scripting languages like Perl, CSS, Javascript, Ajax, and HTML have been used for the development of PDB Explorer. The PDB Explorer directly parses the PDB file, calling methods for parsed element secondary structure element, atoms, coordinates etc. PDB Explorer is freely available at http://www.pdbexplorer.eminentbio.com/home with no requirement of log-in.

NoSQL: collection document and cloud by using a dynamic web query form

NASA Astrophysics Data System (ADS)

Abdalla, Hemn B.; Lin, Jinzhao; Li, Guoquan

2015-07-01

Mongo-DB (from "humongous") is an open-source document database and the leading NoSQL database. A NoSQL (Not Only SQL, next generation databases, being non-relational, deal, open-source and horizontally scalable) presenting a mechanism for storage and retrieval of documents. Previously, we stored and retrieved the data using the SQL queries. Here, we use the MonogoDB that means we are not utilizing the MySQL and SQL queries. Directly importing the documents into our Drives, retrieving the documents on that drive by not applying the SQL queries, using the IO BufferReader and Writer, BufferReader for importing our type of document files to my folder (Drive). For retrieving the document files, the usage is BufferWriter from the particular folder (or) Drive. In this sense, providing the security for those storing files for what purpose means if we store the documents in our local folder means all or views that file and modified that file. So preventing that file, we are furnishing the security. The original document files will be changed to another format like in this paper; Binary format is used. Our documents will be converting to the binary format after that direct storing in one of our folder, that time the storage space will provide the private key for accessing that file. Wherever any user tries to discover the Document files means that file data are in the binary format, the document's file owner simply views that original format using that personal key from receive the secret key from the cloud.

Extra dimensions: 3d and time in pdf documentation

NASA Astrophysics Data System (ADS)

Graf, N. A.

2008-07-01

High energy physics is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide audience. In this talk, we present examples of HEP applications which take advantage of this functionality. We demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input. Using this technique, higher dimensional data, such as LEGO plots or time-dependent information can be included in PDF files. In principle, a complete event display, with full interactivity, can be incorporated into a PDF file. This would allow the end user not only to customize the view and representation of the data, but to access the underlying data itself.

'Isotopo' a database application for facile analysis and management of mass isotopomer data.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eylert, Eva; Eisenreich, Wolfgang; Dandekar, Thomas

2014-01-01

The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application 'Isotopo'. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of (13)C-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. The 'Isotopo' software is available at the following web link (section Download): http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. The package contains three additional files: software executable setup (installer), one data set file (discussed in this article) and one excel file (which can be used to convert data from excel to '.iso' format). The 'Isotopo' software is compatible only with the Microsoft Windows operating system. http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. © The Author(s) 2014. Published by Oxford University Press.

Extra Dimensions: 3D and Time in PDF Documentation

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

Graf, Norman A.; /SLAC

2011-11-10

High energy physics is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standardmore » Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide audience. In this talk, we present examples of HEP applications which take advantage of this functionality. We demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input. Using this technique, higher dimensional data, such as LEGO plots or time-dependent information can be included in PDF files. In principle, a complete event display, with full interactivity, can be incorporated into a PDF file. This would allow the end user not only to customize the view and representation of the data, but to access the underlying data itself.« less

The Design and Usage of the New Data Management Features in NASTRAN

NASA Technical Reports Server (NTRS)

Pamidi, P. R.; Brown, W. K.

1984-01-01

Two new data management features are installed in the April 1984 release of NASTRAN. These two features are the Rigid Format Data Base and the READFILE capability. The Rigid Format Data Base is stored on external files in card image format and can be easily maintained and expanded by the use of standard text editors. This data base provides the user and the NASTRAN maintenance contractor with an easy means for making changes to a Rigid Format or for generating new Rigid Formats without unnecessary compilations and link editing of NASTRAN. Each Rigid Format entry in the data base contains the Direct Matrix Abstraction Program (DMAP), along with the associated restart, DMAP sequence subset and substructure control flags. The READFILE capability allows an user to reference an external secondary file from the NASTRAN primary input file and to read data from this secondary file. There is no limit to the number of external secondary files that may be referenced and read.

Converting laserdisc video to digital video: a demonstration project using brain animations.

PubMed

Jao, C S; Hier, D B; Brint, S U

1995-01-01

Interactive laserdiscs are of limited value in large group learning situations due to the expense of establishing multiple workstations. The authors implemented an alternative to laserdisc video by using indexed digital video combined with an expert system. High-quality video was captured from a laserdisc player and combined with waveform audio into an audio-video-interleave (AVI) file format in the Microsoft Video-for-Windows environment (Microsoft Corp., Seattle, WA). With the use of an expert system, a knowledge-based computer program provided random access to these indexed AVI files. The program can be played on any multimedia computer without the need for laserdiscs. This system offers a high level of interactive video without the overhead and cost of a laserdisc player.

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

PubMed

Moretti, Rocco; Lyskov, Sergey; Das, Rhiju; Meiler, Jens; Gray, Jeffrey J

2018-01-01

The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK a determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org. © 2017 The Protein Society.

FRS Geospatial Return File Format

EPA Pesticide Factsheets

The Geospatial Return File Format describes format that needs to be used to submit latitude and longitude coordinates for use in Envirofacts mapping applications. These coordinates are stored in the Geospatail Reference Tables.

Geologic map of the Sunnymead 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Matti, Jonathan C.

2001-01-01

a. This Readme; includes in Appendix I, data contained in sun_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

SEDIMENT DATA - COMMENCEMENT BAY HYLEBOS WATERWAY - TACOMA, WA - PRE-REMEDIAL DESIGN PROGRAM

EPA Science Inventory

Event 1A/1B Data Files URL address: http://www.epa.gov/r10earth/datalib/superfund/hybos1ab.htm. Sediment Chemistry Data (Database Format): HYBOS1AB.EXE is a self-extracting file which expands to the single-value per record .DBF format database file HYBOS1AB.DBF. This file contai...

76 FR 5431 - Released Rates of Motor Common Carriers of Household Goods

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-31

... may be submitted either via the Board's e-filing format or in traditional paper format. Any person using e-filing should attach a document and otherwise comply with the instructions at the E- FILING link on the Board's website at http://www.stb.dot.gov . Any person submitting a filing in the traditional...

75 FR 52054 - Assessment of Mediation and Arbitration Procedures

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-24

...: Comments may be submitted either via the Board's e-filing format or in the traditional paper format. Any person using e-filing should attach a document and otherwise comply with the instructions at the E-FILING link on the Board's Web site, at http://www.stb.dot.gov . Any person submitting a filing in the...

75 FR 60846 - Bureau of Consular Affairs; Registration for the Diversity Immigrant (DV-2012) Visa Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-01

... need to submit a photo for a child who is already a U.S. citizen or a Legal Permanent Resident. Group... Joint Photographic Experts Group (JPEG) format; it must have a maximum image file size of two hundred... (dpi); the image file format in Joint Photographic Experts Group (JPEG) format; the maximum image file...

78 FR 59743 - Bureau of Consular Affairs; Registration for the Diversity Immigrant (DV-2015) Visa Program

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-27

... already a U.S. citizen or a Lawful Permanent Resident, but you will not be penalized if you do. Group... specifications: Image File Format: The miage must be in the Joint Photographic Experts Group (JPEG) format. Image... in the Joint Photographic Experts Group (JPEG) format. Image File Size: The maximum image file size...

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale

NASA Astrophysics Data System (ADS)

Moore, Josh; Linkert, Melissa; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Li, Simon; Lindner, Dominik; Moore, William J.; Patterson, Andrew J.; Pindelski, Blazej; Ramalingam, Balaji; Rozbicki, Emil; Tarkowska, Aleksandra; Walczysko, Petr; Allan, Chris; Burel, Jean-Marie; Swedlow, Jason

2015-03-01

The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool and OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats and OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research. Bio- Formats reads image data directly from native proprietary formats, bypassing the need for conversion into a standard format. It implements the concept of a file set, a container that defines the contents of multi-dimensional data comprised of many files. OMERO uses Bio-Formats to read files natively, and provides a flexible access mechanism that supports several different storage and access strategies. These new capabilities of OMERO and Bio-Formats make them especially useful for use in imaging applications like digital pathology, high content screening and light sheet microscopy that create routinely large datasets that must be managed and analyzed.

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

PubMed

Rideout, Jai Ram; Chase, John H; Bolyen, Evan; Ackermann, Gail; González, Antonio; Knight, Rob; Caporaso, J Gregory

2016-06-13

Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.

Distributing File-Based Data to Remote Sites Within the BABAR Collaboration

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

Gowdy, Stephen J.

BABAR [1] uses two formats for its data: Objectivity database and root [2] files. This poster concerns the distribution of the latter--for Objectivity data see [3]. The BABAR analysis data is stored in root files--one per physics run and analysis selection channel--maintained in a large directory tree. Currently BABAR has more than 4.5 TBytes in 200,000 root files. This data is (mostly) produced at SLAC, but is required for analysis at universities and research centers throughout the us and Europe. Two basic problems confront us when we seek to import bulk data from slac to an institute's local storage viamore » the network. We must determine which files must be imported (depending on the local site requirements and which files have already been imported), and we must make the optimum use of the network when transferring the data. Basic ftp-like tools (ftp, scp, etc) do not attempt to solve the first problem. More sophisticated tools like rsync [4], the widely-used mirror/synchronization program, compare local and remote file systems, checking for changes (based on file date, size and, if desired, an elaborate checksum) in order to only copy new or modified files. However rsync allows for only limited file selection. Also when, as in BABAR, an extremely large directory structure must be scanned, rsync can take several hours just to determine which files need to be copied. Although rsync (and scp) provides on-the-fly compression, it does not allow us to optimize the network transfer by using multiple streams, adjusting the tcp window size, or separating encrypted authentication from unencrypted data channels.« less

WORM - WINDOWED OBSERVATION OF RELATIVE MOTION

NASA Technical Reports Server (NTRS)

Bauer, F.

1994-01-01

The Windowed Observation of Relative Motion, WORM, program is primarily intended for the generation of simple X-Y plots from data created by other programs. It allows the user to label, zoom, and change the scale of various plots. Three dimensional contour and line plots are provided, although with more limited capabilities. The input data can be in binary or ASCII format, although all data must be in the same format. A great deal of control over the details of the plot is provided, such as gridding, size of tick marks, colors, log/semilog capability, time tagging, and multiple and phase plane plots. Many color and monochrome graphics terminals and hard copy printer/plotters are supported. The WORM executive commands, menu selections and macro files can be used to develop plots and tabular data, query the WORM Help library, retrieve data from input files, and invoke VAX DCL commands. WORM generated plots are displayed on local graphics terminals and can be copied using standard hard copy capabilities. Some of the graphics features of WORM include: zooming and dezooming various portions of the plot; plot documentation including curve labeling and function listing; multiple curves on the same plot; windowing of multiple plots and insets of the same plot; displaying a specific on a curve; and spinning the curve left, right, up, and down. WORM is written in PASCAL for interactive execution and has been implemented on a DEC VAX computer operating under VMS 4.7 with a virtual memory requirement of approximately 392K of 8 bit bytes. It uses the QPLOT device independent graphics library included with WORM. It was developed in 1988.

Accelerating Malware Detection via a Graphics Processing Unit

DTIC Science & Technology

2010-09-01

Processing Unit . . . . . . . . . . . . . . . . . . 4 PE Portable Executable . . . . . . . . . . . . . . . . . . . . . 4 COFF Common Object File Format...operating systems for the future [Szo05]. The PE format is an updated version of the common object file format ( COFF ) [Mic06]. Microsoft released a new...NAs02]. These alerts can be costly in terms of time and resources for individuals and organizations to investigate each misidentified file [YWL07] [Vak10

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data.

PubMed

Clark, Lindsay V; Sacks, Erik J

2016-01-01

In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user-supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.

PubMed

Smelter, Andrey; Astra, Morgan; Moseley, Hunter N B

2017-03-17

The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis. To aid in the use of this public resource, we have developed a package called nmrstarlib in the popular open-source programming language Python. The nmrstarlib's implementation is very efficient, both in design and execution. The library has facilities for reading and writing both NMR-STAR version 2.1 and 3.1 formatted files, parsing them into usable Python dictionary- and list-based data structures, making access and manipulation of the experimental data very natural within Python programs (i.e. "saveframe" and "loop" records represented as individual Python dictionary data structures). Another major advantage of this design is that data stored in original NMR-STAR can be easily converted into its equivalent JavaScript Object Notation (JSON) format, a lightweight data interchange format, facilitating data access and manipulation using Python and any other programming language that implements a JSON parser/generator (i.e., all popular programming languages). We have also developed tools to visualize assigned chemical shift values and to convert between NMR-STAR and JSONized NMR-STAR formatted files. Full API Reference Documentation, User Guide and Tutorial with code examples are also available. We have tested this new library on all current BMRB entries: 100% of all entries are parsed without any errors for both NMR-STAR version 2.1 and version 3.1 formatted files. We also compared our software to three currently available Python libraries for parsing NMR-STAR formatted files: PyStarLib, NMRPyStar, and PyNMRSTAR. The nmrstarlib package is a simple, fast, and efficient library for accessing data from the BMRB. The library provides an intuitive dictionary-based interface with which Python programs can read, edit, and write NMR-STAR formatted files and their equivalent JSONized NMR-STAR files. The nmrstarlib package can be used as a library for accessing and manipulating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STAR file format into its equivalent JSON file format and vice versa, and to visualize chemical shift values. Furthermore, the nmrstarlib implementation provides a guide for effectively JSONizing other older scientific formats, improving the FAIRness of data in these formats.

VizieR Online Data Catalog: SOFIA Massive (SOMA) Star Formation Survey. I. (De Buizer+, 2017)

NASA Astrophysics Data System (ADS)

De Buizer, J. M.; Liu, M.; Tan, J. C.; Zhang, Y.; Beltran, M. T.; Shuping, R.; Staff, J. E.; Tanaka, K. E. I.; Whitney, B.

2018-02-01

The following eight sources, AFGL 4029, AFGL 437, IRAS 07299-1651, G35.20-0.74, G45.45+0.05, IRAS 20126+4104, Cepheus A, and NGC 7538 IRS9, were observed by SOFIA with the FORCAST instrument (see Table 1). Data were taken on multiple flights spanning the Early Science period, Cycle 1, and Cycle 2 SOFIA observing cycles (spanning 2011 May to 2014 June). (4 data files).

Preprocessor that Enables the Use of GridProTM Grids for Unsteady Reynolds-Averaged Navier-Stokes Code TURBO

NASA Technical Reports Server (NTRS)

Shyam, Vikram

2010-01-01

A preprocessor for the Computational Fluid Dynamics (CFD) code TURBO has been developed and tested. The preprocessor converts grids produced by GridPro (Program Development Company (PDC)) into a format readable by TURBO and generates the necessary input files associated with the grid. The preprocessor also generates information that enables the user to decide how to allocate the computational load in a multiple block per processor scenario.

Digital geologic map of the Butler Peak 7.5' quadrangle, San Bernardino County, California

USGS Publications Warehouse

Miller, Fred K.; Matti, Jonathan C.; Brown, Howard J.; digital preparation by Cossette, P. M.

2000-01-01

Open-File Report 00-145, is a digital geologic map database of the Butler Peak 7.5' quadrangle that includes (1) ARC/INFO (Environmental Systems Research Institute) version 7.2.1 Patch 1 coverages, and associated tables, (2) a Portable Document Format (.pdf) file of the Description of Map Units, Correlation of Map Units chart, and an explanation of symbols used on the map, btlrpk_dcmu.pdf, (3) a Portable Document Format file of this Readme, btlrpk_rme.pdf (the Readme is also included as an ascii file in the data package), and (4) a PostScript plot file of the map, Correlation of Map Units, and Description of Map Units on a single sheet, btlrpk.ps. No paper map is included in the Open-File report, but the PostScript plot file (number 4 above) can be used to produce one. The PostScript plot file generates a map, peripheral text, and diagrams in the editorial format of USGS Geologic Investigation Series (I-series) maps.

MXA: a customizable HDF5-based data format for multi-dimensional data sets

NASA Astrophysics Data System (ADS)

Jackson, M.; Simmons, J. P.; De Graef, M.

2010-09-01

A new digital file format is proposed for the long-term archival storage of experimental data sets generated by serial sectioning instruments. The format is known as the multi-dimensional eXtensible Archive (MXA) format and is based on the public domain Hierarchical Data Format (HDF5). The MXA data model, its description by means of an eXtensible Markup Language (XML) file with associated Document Type Definition (DTD) are described in detail. The public domain MXA package is available through a dedicated web site (mxa.web.cmu.edu), along with implementation details and example data files.

An open source Java web application to build self-contained Web GIS sites

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Ahmed, A.; Chassignet, E.; Zavala-Hidalgo, J.

2014-12-01

This work describes OWGIS, an open source Java web application that creates Web GIS sites by automatically writing HTML and JavaScript code. OWGIS is configured by XML files that define which layers (geographic datasets) will be displayed on the websites. This project uses several Open Geospatial Consortium standards to request data from typical map servers, such as GeoServer, and is also able to request data from ncWMS servers. The latter allows for the displaying of 4D data stored using the NetCDF file format (widely used for storing environmental model datasets). Some of the features available on the sites built with OWGIS are: multiple languages, animations, vertical profiles and vertical transects, color palettes, color ranges, and the ability to download data. OWGIS main users are scientists, such as oceanographers or climate scientists, who store their data in NetCDF files and want to analyze, visualize, share, or compare their data using a website.

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

A Summary of Proposed Changes to the Current ICARTT Format Standards and their Implications to Future Airborne Studies

NASA Astrophysics Data System (ADS)

Northup, E. A.; Kusterer, J.; Quam, B.; Chen, G.; Early, A. B.; Beach, A. L., III

2015-12-01

The current ICARTT file format standards were developed for the purpose of fulfilling the data management needs for the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) campaign in 2004. The goal of the ICARTT file format was to establish a common and simple to use data file format to promote data exchange and collaboration among science teams with similar science objectives. ICARTT has been the NASA standard since 2010, and is widely used by NOAA, NSF, and international partners (DLR, FAAM). Despite its level of acceptance, there are a number of issues with the current ICARTT format, especially concerning the machine readability. To enhance usability, the ICARTT Refresh Earth Science Data Systems Working Group (ESDSWG) was established to enable a platform for atmospheric science data producers, users (e.g. modelers) and data managers to collaborate on developing criteria for this file format. Ultimately, this is a cross agency effort to improve and aggregate the metadata records being produced. After conducting a survey to identify deficiencies in the current format, we determined which are considered most important to the various communities. Numerous recommendations were made to improve upon the file format while maintaining backward compatibility. The recommendations made to date and their advantages and limitations will be discussed.

NASA Standard for Airborne Data: ICARTT Format ESDS-RFC-019

NASA Astrophysics Data System (ADS)

Thornhill, A.; Brown, C.; Aknan, A.; Crawford, J. H.; Chen, G.; Williams, E. J.

2011-12-01

Airborne field studies generate a plethora of data products in the effort to study atmospheric composition and processes. Data file formats for airborne field campaigns are designed to present data in an understandable and organized way to support collaboration and to document relevant and important meta data. The ICARTT file format was created to facilitate data management during the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) campaign in 2004 that involved government-agencies and university participants from five countries. Since this mission the ICARTT format has been used in subsequent field campaigns such as Polar Study Using Aircraft Remote Sensing, Surface Measurements and Models of Climates, Chemistry, Aerosols, and Transport (POLARCAT) and the first phase of Deriving Information on Surface Conditions from COlumn and VERtically Resolved Observations Relevant to Air Quality (DISCOVER-AQ). The ICARTT file format has been endorsed as a standard format for airborne data by the Standard Process Group (SPG), one of the Earth Science Data Systems Working Groups (ESDSWG) in 2010. The detailed description of the ICARTT format can be found at http://www-air.larc.nasa.gov/missions/etc/ESDS-RFC-019-v1.00.pdf. The ICARTT data format is an ASCII, comma delimited format that was based on the NASA Ames and GTE file formats. The file header is detailed enough to fully describe the data for users outside of the instrument group and includes a description of the meta data. The ICARTT scanning tools, format structure, implementations, and examples will be presented.

Viewing Files | Smokefree 60+

Cancer.gov

In addition to standard HTML webpages, our website contains files in other formats. You may need additional software or browser plug-ins to view some of these files. The following list shows each format along with links to the corresponding freely available plug-ins or viewers. Documents  Adobe Acrobat Reader (.pdf)

Dependency Tree Annotation Software

DTIC Science & Technology

2015-11-01

formats, and it provides numerous options for customizing how dependency trees are displayed. Built entirely in Java , it can run on a wide range of...tree can be saved as an image, .mxe (a mxGraph editing file), a .conll file, and several other file formats. DTE uses the open source Java version

Challenges for data storage in medical imaging research.

PubMed

Langer, Steve G

2011-04-01

Researchers in medical imaging have multiple challenges for storing, indexing, maintaining viability, and sharing their data. Addressing all these concerns requires a constellation of tools, but not all of them need to be local to the site. In particular, the data storage challenges faced by researchers can begin to require professional information technology skills. With limited human resources and funds, the medical imaging researcher may be better served with an outsourcing strategy for some management aspects. This paper outlines an approach to manage the main objectives faced by medical imaging scientists whose work includes processing and data mining on non-standard file formats, and relating those files to the their DICOM standard descendents. The capacity of the approach scales as the researcher's need grows by leveraging the on-demand provisioning ability of cloud computing.

Improving the interactivity and functionality of Web-based radiology teaching files with the Java programming language.

PubMed

Eng, J

1997-01-01

Java is a programming language that runs on a "virtual machine" built into World Wide Web (WWW)-browsing programs on multiple hardware platforms. Web pages were developed with Java to enable Web-browsing programs to overlay transparent graphics and text on displayed images so that the user could control the display of labels and annotations on the images, a key feature not available with standard Web pages. This feature was extended to include the presentation of normal radiologic anatomy. Java programming was also used to make Web browsers compatible with the Digital Imaging and Communications in Medicine (DICOM) file format. By enhancing the functionality of Web pages, Java technology should provide greater incentive for using a Web-based approach in the development of radiology teaching material.

User's guide to HYPOINVERSE-2000, a Fortran program to solve for earthquake locations and magnitudes

USGS Publications Warehouse

Klein, Fred W.

2002-01-01

Hypoinverse is a computer program that processes files of seismic station data for an earthquake (like p wave arrival times and seismogram amplitudes and durations) into earthquake locations and magnitudes. It is one of a long line of similar USGS programs including HYPOLAYR (Eaton, 1969), HYPO71 (Lee and Lahr, 1972), and HYPOELLIPSE (Lahr, 1980). If you are new to Hypoinverse, you may want to start by glancing at the section “SOME SIMPLE COMMAND SEQUENCES” to get a feel of some simpler sessions. This document is essentially an advanced user’s guide, and reading it sequentially will probably plow the reader into more detail than he/she needs. Every user must have a crust model, station list and phase data input files, and glancing at these sections is a good place to begin. The program has many options because it has grown over the years to meet the needs of one the largest seismic networks in the world, but small networks with just a few stations do use the program and can ignore most of the options and commands. History and availability. Hypoinverse was originally written for the Eclipse minicomputer in 1978 (Klein, 1978). A revised version for VAX and Pro-350 computers (Klein, 1985) was later expanded to include multiple crustal models and other capabilities (Klein, 1989). This current report documents the expanded Y2000 version and it supercedes the earlier documents. It serves as a detailed user's guide to the current version running on unix and VAX-alpha computers, and to the version supplied with the Earthworm earthquake digitizing system. Fortran-77 source code (Sun and VAX compatible) and copies of this documentation is available via anonymous ftp from computers in Menlo Park. At present, the computer is swave.wr.usgs.gov and the directory is /ftp/pub/outgoing/klein/hyp2000. If you are running Hypoinverse on one of the Menlo Park EHZ or NCSN unix computers, the executable currently is ~klein/hyp2000/hyp2000. New features. The Y2000 version of Hypoinverse includes all of the previous capabilities, but adds Y2000 formats to those defined earlier. In most cases, the new formats add 2 digits to the year field to accommodate the century. Other fields are sometimes rearranged or expanded to accommodate a better field order. The Y2000 formats are invoked with the “200” command. When the Y2000 flag is turned on, all files are read and written in the new format and there is no mixing of format types in a single run. Some formats without a date field, like station files, have not changed. A separate program called 2000CONV has been written to convert old formats to new. Other new features, like expanded station names, calculating amplitude magnitudes from a variety of digital seismometers, station history files, interactive earthquake processing, and locations from CUSP (Caltech USGS Seismic Processing) binary files have been added. General features. Hypoinverse will locate any number of events in an input file, which can be in one of several different formats. Any or all of printout, summary or archive output may be produced. Hypoinverse is driven by user commands. The various commands define input and output files, set adjustable parameters, and solve for locations of a file of earthquake data using the parameters and files currently set. It is both interactive and "batch" in that commands may be executed either from the keyboard or from a file. You execute the commands in a file by typing @filename at the Hypoinverse prompt. Users may either supply parameters on the command line, or omit them and are prompted interactively. The current parameter values are displayed and may be taken as defaults by pressing just the RETURN key after the prompt. This makes the program very easy to use, providing you can remember the names of the commands. Combining commands with and without their required parameters into a command file permits a variety of customized procedures such as automatic input of crustal model and station data, but prompting for a different phase file each time. All commands are 3 letters long and most require one or more parameters or file names. If they appear on a line with a command, character strings such as filenames must be enclosed in apostrophes (single quotes). Appendix 1 gives this and other free-format rules for supplying parameters, which are parsed in Fortran. When several parameters are required following a command, any of them may be omitted by replacing them with null fields (see appendix 1). A null field leaves that parameter unchanged from its current or default value. When you start HYPOINVERSE, default values are in effect for all parameters except file names. Hypoinverse is a complicated program with many features and options. Many of these "advanced" or seldom used features are documented here, but are more detailed than a typical user needs to read about when first starting with the program. I have put some of this material in smaller type so that a first time user can concentrate on the more important information.

An Innovative Open Data-driven Approach for Improved Interpretation of Coverage Data at NASA JPL's PO.DAA

NASA Astrophysics Data System (ADS)

McGibbney, L. J.; Armstrong, E. M.

2016-12-01

Figuratively speaking, Scientific Datasets (SD) are shared by data producers in a multitude of shapes, sizes and flavors. Primarily however they exist as machine-independent manifestations supporting the creation, access, and sharing of array-oriented SD that can on occasion be spread across multiple files. Within the Earth Sciences, the most notable general examples include the HDF family, NetCDF, etc. with other formats such as GRIB being used pervasively within specific domains such as the Oceanographic, Atmospheric and Meteorological sciences. Such file formats contain Coverage Data e.g. a digital representation of some spatio-temporal phenomenon. A challenge for large data producers such as NASA and NOAA as well as consumers of coverage datasets (particularly surrounding visualization and interactive use within web clients) is that this is still not a straight-forward issue due to size, serialization and inherent complexity. Additionally existing data formats are either unsuitable for the Web (like netCDF files) or hard to interpret independently due to missing standard structures and metadata (e.g. the OPeNDAP protocol). Therefore alternative, Web friendly manifestations of such datasets are required.CoverageJSON is an emerging data format for publishing coverage data to the web in a web-friendly, way which fits in with the linked data publication paradigm hence lowering the barrier for interpretation by consumers via mobile devices and client applications, etc. as well as data producers who can build next generation Web friendly Web services around datasets. This work will detail how CoverageJSON is being evaluated at NASA JPL's PO.DAAC as an enabling data representation format for publishing SD as Linked Open Data embedded within SD landing pages as well as via semantic data repositories. We are currently evaluating how utilization of CoverageJSON within SD landing pages addresses the long-standing acknowledgement that SD producers are not currently addressing content-based optimization within their SD landing pages for better crawlability by commercial search engines.

Representation of thermal infrared imaging data in the DICOM using XML configuration files.

PubMed

Ruminski, Jacek

2007-01-01

The DICOM standard has become a widely accepted and implemented format for the exchange and storage of medical imaging data. Different imaging modalities are supported however there is not a dedicated solution for thermal infrared imaging in medicine. In this article we propose new ideas and improvements to final proposal of the new DICOM Thermal Infrared Imaging structures and services. Additionally, we designed, implemented and tested software packages for universal conversion of existing thermal imaging files to the DICOM format using XML configuration files. The proposed solution works fast and requires minimal number of user interactions. The XML configuration file enables to compose a set of attributes for any source file format of thermal imaging camera.

An Open Software Platform for Sharing Water Resource Models, Code and Data

NASA Astrophysics Data System (ADS)

Knox, Stephen; Meier, Philipp; Mohamed, Khaled; Korteling, Brett; Matrosov, Evgenii; Huskova, Ivana; Harou, Julien; Rosenberg, David; Tilmant, Amaury; Medellin-Azuara, Josue; Wicks, Jon

2016-04-01

The modelling of managed water resource systems requires new approaches in the face of increasing future uncertainty. Water resources management models, even if applied to diverse problem areas, use common approaches such as representing the problem as a network of nodes and links. We propose a data management software platform, called Hydra, that uses this commonality to allow multiple models using a node-link structure to be managed and run using a single software system. Hydra's user interface allows users to manage network topology and associated data. Hydra feeds this data directly into a model, importing from and exporting to different file formats using Apps. An App connects Hydra to a custom model, a modelling system such as GAMS or MATLAB or to different file formats such as MS Excel, CSV and ESRI Shapefiles. Hydra allows users to manage their data in a single, consistent place. Apps can be used to run domain-specific models and allow users to work with their own required file formats. The Hydra App Store offers a collaborative space where model developers can publish, review and comment on Apps, models and data. Example Apps and open-source libraries are available in a variety of languages (Python, Java and .NET). The App Store can act as a hub for water resource modellers to view and share Apps, models and data easily. This encourages an ecosystem of development using a shared platform, resulting in more model integration and potentially greater unity within resource modelling communities. www.hydraplatform.org www.hydraappstore.com

SNPConvert: SNP Array Standardization and Integration in Livestock Species.

PubMed

Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

2016-06-09

One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.

Multiple autoclave cycles affect the surface of rotary nickel-titanium files: an atomic force microscopy study.

PubMed

Valois, Caroline R A; Silva, Luciano P; Azevedo, Ricardo B

2008-07-01

The purpose of this study was to evaluate the surface of rotary nickel-titanium (Ni-Ti) files after multiple autoclave cycles. Two different types of rotary Ni-Ti (Greater Taper and ProFile) were attached to a glass base. After 1, 5, and 10 autoclave cycles the files were positioned in the atomic force microscope. The analyses were performed on 15 different points. The same files were used as control before any autoclave cycle. The following vertical topographic parameters were measured: arithmetic mean roughness, maximum height, and root mean square. The differences were tested by analysis of variance with Tukey test. All topographic parameters were higher for both Greater Taper and ProFile after 10 cycles compared with the control (P < .05). ProFile also showed higher topographic parameters after 5 cycles compared with the control (P < .05). The results indicated that multiple autoclave cycles increase the depth of surface irregularities located on rotary Ni-Ti files.

Preliminary geologic map of the Perris 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Digital preparation by Bovard, Kelly R.; Alvarez, Rachel M.

2003-01-01

Open-File Report 03-270 contains a digital geologic map database of the Perris 7.5’ quadrangle, Riverside County, California that includes: 1. ARC/INFO (Environmental Systems Research Institute, http://www.esri.com) version 7.2.1 coverages of the various elements of the geologic map. 2. A Postscript file to plot the geologic map on a topographic base, and containing a Correlation of Map Units diagram (CMU), a Description of Map Units (DMU), and an index map. 3. Portable Document Format (.pdf) files of: a. A Readme file b. The same graphic as described in 2 above. Test plots have not produced precise 1:24,000- scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formationname, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc.

Geologic map of the Riverside East 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Cox, Brett F.

2001-01-01

a. This Readme; includes in Appendix I, data contained in rse_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Corona North 7.5' quadrangle, Riverside and San Bernardino counties, California

USGS Publications Warehouse

Morton, Douglas M.; Gray, C.H.; Bovard, Kelly R.; Dawson, Michael

2002-01-01

a. This Readme; includes in Appendix I, data contained in crn_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced precise 1:24,000- scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Lake Mathews 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Weber, F. Harold

2001-01-01

a. This Readme; includes in Appendix I, data contained in lkm_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Miscellaneous Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous.Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand.In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Steele Peak 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; digital preparation by Alvarez, Rachel M.; Diep, Van M.

2001-01-01

a. This Readme; includes in Appendix I, data contained in stp_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Geologic map of the Riverside West 7.5' quadrangle, Riverside County, California

USGS Publications Warehouse

Morton, Douglas M.; Cox, Brett F.

2001-01-01

a. This Readme; includes in Appendix I, data contained in rsw_met.txt b. The same graphic as plotted in 2 above. Test plots have not produced 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Marine deposits are in part overlain by local, mostly alluvial fan, deposits and are labeled Qomf. Grain size follows f.Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3b above) or plotting the postscript file (2 above).

Transported Geothermal Energy Technoeconomic Screening Tool - Calculation Engine

DOE Data Explorer

Liu, Xiaobing

2016-09-21

This calculation engine estimates technoeconomic feasibility for transported geothermal energy projects. The TGE screening tool (geotool.exe) takes input from input file (input.txt), and list results into output file (output.txt). Both the input and ouput files are in the same folder as the geotool.exe. To use the tool, the input file containing adequate information of the case should be prepared in the format explained below, and the input file should be put into the same folder as geotool.exe. Then the geotool.exe can be executed, which will generate a output.txt file in the same folder containing all key calculation results. The format and content of the output file is explained below as well.

Effect of Instrumentation Length and Instrumentation Systems: Hand Versus Rotary Files on Apical Crack Formation – An In vitro Study

PubMed Central

Mahesh, MC; Bhandary, Shreetha

2017-01-01

Introduction Stresses generated during root canal instrumentation have been reported to cause apical cracks. The smaller, less pronounced defects like cracks can later propagate into vertical root fracture, when the tooth is subjected to repeated stresses from endodontic or restorative procedures. Aim This study evaluated occurrence of apical cracks with stainless steel hand files, rotary NiTi RaCe and K3 files at two different instrumentation lengths. Materials and Methods In the present in vitro study, 60 mandibular premolars were mounted in resin blocks with simulated periodontal ligament. Apical 3 mm of the root surfaces were exposed and stained using India ink. Preoperative images of root apices were obtained at 100x using stereomicroscope. The teeth were divided into six groups of 10 each. First two groups were instrumented with stainless steel files, next two groups with rotary NiTi RaCe files and the last two groups with rotary NiTi K3 files. The instrumentation was carried out till the apical foramen (Working Length-WL) and 1 mm short of the apical foramen (WL-1) with each file system. After root canal instrumentation, postoperative images of root apices were obtained. Preoperative and postoperative images were compared and the occurrence of cracks was recorded. Descriptive statistical analysis and Chi-square tests were used to analyze the results. Results Apical root cracks were seen in 30%, 35% and 20% of teeth instrumented with K-files, RaCe files and K3 files respectively. There was no statistical significance among three instrumentation systems in the formation of apical cracks (p=0.563). Apical cracks were seen in 40% and 20% of teeth instrumented with K-files; 60% and 10% of teeth with RaCe files and 40% and 0% of teeth with K3 files at WL and WL-1 respectively. For groups instrumented with hand files there was no statistical significance in number of cracks at WL and WL-1 (p=0.628). But for teeth instrumented with RaCe files and K3 files significantly more number of cracks were seen at WL than WL-1 (p=0.057 for RaCe files and p=0.087 for K3 files). Conclusion There was no statistical significance between stainless steel hand files and rotary files in terms of crack formation. Instrumentation length had a significant effect on the formation of cracks when rotary files were used. Using rotary instruments 1 mm short of apical foramen caused lesser crack formation. But, there was no statistically significant difference in number of cracks formed with hand files at two instrumentation levels. PMID:28274036

Effect of Instrumentation Length and Instrumentation Systems: Hand Versus Rotary Files on Apical Crack Formation - An In vitro Study.

PubMed

Devale, Madhuri R; Mahesh, M C; Bhandary, Shreetha

2017-01-01

Stresses generated during root canal instrumentation have been reported to cause apical cracks. The smaller, less pronounced defects like cracks can later propagate into vertical root fracture, when the tooth is subjected to repeated stresses from endodontic or restorative procedures. This study evaluated occurrence of apical cracks with stainless steel hand files, rotary NiTi RaCe and K3 files at two different instrumentation lengths. In the present in vitro study, 60 mandibular premolars were mounted in resin blocks with simulated periodontal ligament. Apical 3 mm of the root surfaces were exposed and stained using India ink. Preoperative images of root apices were obtained at 100x using stereomicroscope. The teeth were divided into six groups of 10 each. First two groups were instrumented with stainless steel files, next two groups with rotary NiTi RaCe files and the last two groups with rotary NiTi K3 files. The instrumentation was carried out till the apical foramen (Working Length-WL) and 1 mm short of the apical foramen (WL-1) with each file system. After root canal instrumentation, postoperative images of root apices were obtained. Preoperative and postoperative images were compared and the occurrence of cracks was recorded. Descriptive statistical analysis and Chi-square tests were used to analyze the results. Apical root cracks were seen in 30%, 35% and 20% of teeth instrumented with K-files, RaCe files and K3 files respectively. There was no statistical significance among three instrumentation systems in the formation of apical cracks (p=0.563). Apical cracks were seen in 40% and 20% of teeth instrumented with K-files; 60% and 10% of teeth with RaCe files and 40% and 0% of teeth with K3 files at WL and WL-1 respectively. For groups instrumented with hand files there was no statistical significance in number of cracks at WL and WL-1 (p=0.628). But for teeth instrumented with RaCe files and K3 files significantly more number of cracks were seen at WL than WL-1 (p=0.057 for RaCe files and p=0.087 for K3 files). There was no statistical significance between stainless steel hand files and rotary files in terms of crack formation. Instrumentation length had a significant effect on the formation of cracks when rotary files were used. Using rotary instruments 1 mm short of apical foramen caused lesser crack formation. But, there was no statistically significant difference in number of cracks formed with hand files at two instrumentation levels.

15 CFR 995.26 - Conversion of NOAA ENC ® files to other formats.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Conversion of NOAA ENC files to other formats—(1) Content. CEVAD may provide NOAA ENC data in forms other... data files without degradation to positional accuracy or informational content. (2) Software certification. Conversion of NOAA ENC data to other formats must be accomplished within the constraints of IHO...

Early Detection | Division of Cancer Prevention

Cancer.gov

[[{"fid":"171","view_mode":"default","fields":{"format":"default","field_file_image_alt_text[und][0][value]":"Early Detection Research Group Homepage Logo","field_file_image_title_text[und][0][value]":"Early Detection Research Group Homepage Logo","field_folder[und]":"15"},"type":"media","field_deltas":{"1":{"format":"default","field_file_image_alt_text[und][0][value]":"Early

Image Size Variation Influence on Corrupted and Non-viewable BMP Image

NASA Astrophysics Data System (ADS)

Azmi, Tengku Norsuhaila T.; Azma Abdullah, Nurul; Rahman, Nurul Hidayah Ab; Hamid, Isredza Rahmi A.; Chai Wen, Chuah

2017-08-01

Image is one of the evidence component seek in digital forensics. Joint Photographic Experts Group (JPEG) format is most popular used in the Internet because JPEG files are very lossy and easy to compress that can speed up Internet transmitting processes. However, corrupted JPEG images are hard to recover due to the complexities of determining corruption point. Nowadays Bitmap (BMP) images are preferred in image processing compared to another formats because BMP image contain all the image information in a simple format. Therefore, in order to investigate the corruption point in JPEG, the file is required to be converted into BMP format. Nevertheless, there are many things that can influence the corrupting of BMP image such as the changes of image size that make the file non-viewable. In this paper, the experiment indicates that the size of BMP file influences the changes in the image itself through three conditions, deleting, replacing and insertion. From the experiment, we learnt by correcting the file size, it can able to produce a viewable file though partially. Then, it can be investigated further to identify the corruption point.

Operational Interoperable Web Coverage Service for Earth Observing Satellite Data: Issues and Lessons Learned

NASA Astrophysics Data System (ADS)

Yang, W.; Min, M.; Bai, Y.; Lynnes, C.; Holloway, D.; Enloe, Y.; di, L.

2008-12-01

In the past few years, there have been growing interests, among major earth observing satellite (EOS) data providers, in serving data through the interoperable Web Coverage Service (WCS) interface protocol, developed by the Open Geospatial Consortium (OGC). The interface protocol defined in WCS specifications allows client software to make customized requests of multi-dimensional EOS data, including spatial and temporal subsetting, resampling and interpolation, and coordinate reference system (CRS) transformation. A WCS server describes an offered coverage, i.e., a data product, through a response to a client's DescribeCoverage request. The description includes the offered coverage's spatial/temporal extents and resolutions, supported CRSs, supported interpolation methods, and supported encoding formats. Based on such information, a client can request the entire or a subset of coverage in any spatial/temporal resolutions and in any one of the supported CRSs, formats, and interpolation methods. When implementing a WCS server, a data provider has different approaches to present its data holdings to clients. One of the most straightforward, and commonly used, approaches is to offer individual physical data files as separate coverages. Such implementation, however, will result in too many offered coverages for large data holdings and it also cannot fully present the relationship among different, but spatially and/or temporally associated, data files. It is desirable to disconnect offered coverages from physical data files so that the former is more coherent, especially in spatial and temporal domains. Therefore, some servers offer one single coverage for a set of spatially coregistered time series data files such as a daily global precipitation coverage linked to many global single- day precipitation files; others offer one single coverage for multiple temporally coregistered files together forming a large spatial extent. In either case, a server needs to assemble an output coverage real-time by combining potentially large number of physical files, which can be operationally difficult. The task becomes more challenging if an offered coverage involves spatially and temporally un-registered physical files. In this presentation, we will discuss issues and lessons learned in providing NASA's AIRS Level 2 atmospheric products, which are in satellite swath CRS and in 6-minute segment granule files, as virtual global coverages. We"ll discuss the WCS server's on- the-fly georectification, mosaicking, quality screening, performance, and scalability.

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

Ingargiola, A.; Laurence, T. A.; Boutelle, R.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Informatics in radiology: automated structured reporting of imaging findings using the AIM standard and XML.

PubMed

Zimmerman, Stefan L; Kim, Woojin; Boonn, William W

2011-01-01

Quantitative and descriptive imaging data are a vital component of the radiology report and are frequently of paramount importance to the ordering physician. Unfortunately, current methods of recording these data in the report are both inefficient and error prone. In addition, the free-text, unstructured format of a radiology report makes aggregate analysis of data from multiple reports difficult or even impossible without manual intervention. A structured reporting work flow has been developed that allows quantitative data created at an advanced imaging workstation to be seamlessly integrated into the radiology report with minimal radiologist intervention. As an intermediary step between the workstation and the reporting software, quantitative and descriptive data are converted into an extensible markup language (XML) file in a standardized format specified by the Annotation and Image Markup (AIM) project of the National Institutes of Health Cancer Biomedical Informatics Grid. The AIM standard was created to allow image annotation data to be stored in a uniform machine-readable format. These XML files containing imaging data can also be stored on a local database for data mining and analysis. This structured work flow solution has the potential to improve radiologist efficiency, reduce errors, and facilitate storage of quantitative and descriptive imaging data for research. Copyright © RSNA, 2011.

UFO (UnFold Operator) default data format

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

Kissel, L.; Biggs, F.; Marking, T.R.

The default format for the storage of x,y data for use with the UFO code is described. The format assumes that the data stored in a file is a matrix of values; two columns of this matrix are selected to define a function of the form y = f(x). This format is specifically designed to allow for easy importation of data obtained from other sources, or easy entry of data using a text editor, with a minimum of reformatting. This format is flexible and extensible through the use of inline directives stored in the optional header of the file. Amore » special extension of the format implements encoded data which significantly reduces the storage required as compared wth the unencoded form. UFO supports several extensions to the file specification that implement execute-time operations, such as, transformation of the x and/or y values, selection of specific columns of the matrix for association with the x and y values, input of data directly from other formats (e.g., DAMP and PFF), and a simple type of library-structured file format. Several examples of the use of the format are given.« less

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

PubMed

McDonald, Daniel; Clemente, Jose C; Kuczynski, Justin; Rideout, Jai Ram; Stombaugh, Jesse; Wendel, Doug; Wilke, Andreas; Huse, Susan; Hufnagle, John; Meyer, Folker; Knight, Rob; Caporaso, J Gregory

2012-07-12

We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.

Development of a web-based DICOM-SR viewer for CAD data of multiple sclerosis lesions in an imaging informatics-based efolder

NASA Astrophysics Data System (ADS)

Ma, Kevin; Wong, Jonathan; Zhong, Mark; Zhang, Jeff; Liu, Brent

2014-03-01

In the past, we have presented an imaging-informatics based eFolder system for managing and analyzing imaging and lesion data of multiple sclerosis (MS) patients, which allows for data storage, data analysis, and data mining in clinical and research settings. The system integrates the patient's clinical data with imaging studies and a computer-aided detection (CAD) algorithm for quantifying MS lesion volume, lesion contour, locations, and sizes in brain MRI studies. For compliance with IHE integration protocols, long-term storage in PACS, and data query and display in a DICOM compliant clinical setting, CAD results need to be converted into DICOM-Structured Report (SR) format. Open-source dcmtk and customized XML templates are used to convert quantitative MS CAD results from MATLAB to DICOM-SR format. A web-based GUI based on our existing web-accessible DICOM object (WADO) image viewer has been designed to display the CAD results from generated SR files. The GUI is able to parse DICOM-SR files and extract SR document data, then display lesion volume, location, and brain matter volume along with the referenced DICOM imaging study. In addition, the GUI supports lesion contour overlay, which matches a detected MS lesion with its corresponding DICOM-SR data when a user selects either the lesion or the data. The methodology of converting CAD data in native MATLAB format to DICOM-SR and displaying the tabulated DICOM-SR along with the patient's clinical information, and relevant study images in the GUI will be demonstrated. The developed SR conversion model and GUI support aim to further demonstrate how to incorporate CAD post-processing components in a PACS and imaging informatics-based environment.

76 FR 23222 - Electric Reliability Organization Interpretation of Transmission Operations Reliability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-26

... applications or print-to-PDF format, and not in a scanned format, at http://www.ferc.gov/docs-filing/efiling....3d 1342 (DC Cir. 2009). \\5\\ Mandatory Reliability Standards for the Bulk-Power System, Order No. 693... applications or print-to-PDF format and not in a scanned format. Commenters filing electronically do not need...

File concepts for parallel I/O

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.

1989-01-01

The subject of input/output (I/O) was often neglected in the design of parallel computer systems, although for many problems I/O rates will limit the speedup attainable. The I/O problem is addressed by considering the role of files in parallel systems. The notion of parallel files is introduced. Parallel files provide for concurrent access by multiple processes, and utilize parallelism in the I/O system to improve performance. Parallel files can also be used conventionally by sequential programs. A set of standard parallel file organizations is proposed, organizations are suggested, using multiple storage devices. Problem areas are also identified and discussed.

Facilitating Analysis of Multiple Partial Data Streams

NASA Technical Reports Server (NTRS)

Maimone, Mark W.; Liebersbach, Robert R.

2008-01-01

Robotic Operations Automation: Mechanisms, Imaging, Navigation report Generation (ROAMING) is a set of computer programs that facilitates and accelerates both tactical and strategic analysis of time-sampled data especially the disparate and often incomplete streams of Mars Explorer Rover (MER) telemetry data described in the immediately preceding article. As used here, tactical refers to the activities over a relatively short time (one Martian day in the original MER application) and strategic refers to a longer time (the entire multi-year MER missions in the original application). Prior to installation, ROAMING must be configured with the types of data of interest, and parsers must be modified to understand the format of the input data (many example parsers are provided, including for general CSV files). Thereafter, new data from multiple disparate sources are automatically resampled into a single common annotated spreadsheet stored in a readable space-separated format, and these data can be processed or plotted at any time scale. Such processing or plotting makes it possible to study not only the details of a particular activity spanning only a few seconds, but also longer-term trends. ROAMING makes it possible to generate mission-wide plots of multiple engineering quantities [e.g., vehicle tilt as in Figure 1(a), motor current, numbers of images] that, heretofore could be found only in thousands of separate files. ROAMING also supports automatic annotation of both images and graphs. In the MER application, labels given to terrain features by rover scientists and engineers are automatically plotted in all received images based on their associated camera models (see Figure 2), times measured in seconds are mapped to Mars local time, and command names or arbitrary time-labeled events can be used to label engineering plots, as in Figure 1(b).

Preliminary geologic map of the Fontana 7.5' quadrangle, Riverside and San Bernardino Counties, California

USGS Publications Warehouse

Morton, Douglas M.; Digital preparation by Bovard, Kelly R.

2003-01-01

Open-File Report 03-418 is a digital geologic data set that maps and describes the geology of the Fontana 7.5’ quadrangle, Riverside and San Bernardino Counties, California. The Fontana quadrangle database is one of several 7.5’ quadrangle databases that are being produced by the Southern California Areal Mapping Project (SCAMP). These maps and databases are, in turn, part of the nation-wide digital geologic map coverage being developed by the National Cooperative Geologic Map Program of the U.S. Geological Survey (USGS). General Open-File Report 03-418 contains a digital geologic map database of the Fontana 7.5’ quadrangle, Riverside and San Bernardino Counties, California that includes: 1. ARC/INFO (Environmental Systems Research Institute, http://www.esri.com) version 7.2.1 coverages of the various elements of the geologic map. 2. A Postscript file (fon_map.ps) to plot the geologic map on a topographic base, and containing a Correlation of Map Units diagram (CMU), a Description of Map Units (DMU), and an index map. 3. An Encapsulated PostScript (EPS) file (fon_grey.eps) created in Adobe Illustrator 10.0 to plot the geologic map on a grey topographic base, and containing a Correlation of Map Units (CMU), a Description of Map Units (DMU), and an index map. 4. Portable Document Format (.pdf) files of: a. the Readme file; includes in Appendix I, data contained in fon_met.txt b. The same graphics as plotted in 2 and 3 above.Test plots have not produced precise 1:24,000-scale map sheets. Adobe Acrobat page size setting influences map scale. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Where known, grain size is indicated on the map by a subscripted letter or letters following the unit symbols as follows: lg, large boulders; b, boulder; g, gravel; a, arenaceous; s, silt; c, clay; e.g. Qyfa is a predominantly young alluvial fan deposit that is arenaceous. Multiple letters are used for more specific identification or for mixed units, e.g., Qfysa is a silty sand. In some cases, mixed units are indicated by a compound symbol; e.g., Qyf2sc. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (4b above) or plotting the postscript files (2 or 3 above).

NetpathXL - An Excel Interface to the Program NETPATH

USGS Publications Warehouse

Parkhurst, David L.; Charlton, Scott R.

2008-01-01

NetpathXL is a revised version of NETPATH that runs under Windows? operating systems. NETPATH is a computer program that uses inverse geochemical modeling techniques to calculate net geochemical reactions that can account for changes in water composition between initial and final evolutionary waters in hydrologic systems. The inverse models also can account for the isotopic composition of waters and can be used to estimate radiocarbon ages of dissolved carbon in ground water. NETPATH relies on an auxiliary, database program, DB, to enter the chemical analyses and to perform speciation calculations that define total concentrations of elements, charge balance, and redox state of aqueous solutions that are then used in inverse modeling. Instead of DB, NetpathXL relies on Microsoft Excel? to enter the chemical analyses. The speciation calculation formerly included in DB is implemented within the program NetpathXL. A program DBXL can be used to translate files from the old DB format (.lon files) to NetpathXL spreadsheets, or to create new NetpathXL spreadsheets. Once users have a NetpathXL spreadsheet with the proper format, new spreadsheets can be generated by copying or saving NetpathXL spreadsheets. In addition, DBXL can convert NetpathXL spreadsheets to PHREEQC input files. New capabilities in PHREEQC (version 2.15) allow solution compositions to be written to a .lon file, and inverse models developed in PHREEQC to be written as NetpathXL .pat and model files. NetpathXL can open NetpathXL spreadsheets, NETPATH-format path files (.pat files), and NetpathXL-format path files (.pat files). Once the speciation calculations have been performed on a spreadsheet file or a .pat file has been opened, the NetpathXL calculation engine is identical to the original NETPATH. Development of models and viewing results in NetpathXL rely on keyboard entry as in NETPATH.

17 CFR 232.202 - Continuing hardship exemption.

Code of Federal Regulations, 2010 CFR

2010-04-01

... electronic format or post the Interactive Data File on its corporate Web site, as applicable, on the required... Interactive Data File, the electronic filer need not post on its Web site any statement with regard to the... submitted in electronic format or, in the case of an Interactive Data File (§ 232.11), to be posted on the...

17 CFR 232.202 - Continuing hardship exemption.

Code of Federal Regulations, 2013 CFR

2013-04-01

... electronic format or post the Interactive Data File on its corporate Web site, as applicable, on the required... Interactive Data File, the electronic filer need not post on its Web site any statement with regard to the... submitted in electronic format or, in the case of an Interactive Data File (§ 232.11), to be posted on the...

17 CFR 232.202 - Continuing hardship exemption.

Code of Federal Regulations, 2012 CFR

2012-04-01

... electronic format or post the Interactive Data File on its corporate Web site, as applicable, on the required... Interactive Data File, the electronic filer need not post on its Web site any statement with regard to the... submitted in electronic format or, in the case of an Interactive Data File (§ 232.11), to be posted on the...

17 CFR 232.202 - Continuing hardship exemption.

Code of Federal Regulations, 2014 CFR

2014-04-01

... electronic format or post the Interactive Data File on its corporate Web site, as applicable, on the required... Interactive Data File, the electronic filer need not post on its Web site any statement with regard to the... submitted in electronic format or, in the case of an Interactive Data File (§ 232.11), to be posted on the...

17 CFR 232.202 - Continuing hardship exemption.

Code of Federal Regulations, 2011 CFR

2011-04-01

... electronic format or post the Interactive Data File on its corporate Web site, as applicable, on the required... Interactive Data File, the electronic filer need not post on its Web site any statement with regard to the... submitted in electronic format or, in the case of an Interactive Data File (§ 232.11), to be posted on the...

Data Science Bowl Launched to Improve Lung Cancer Screening | Division of Cancer Prevention

Cancer.gov

[[{"fid":"2078","view_mode":"default","fields":{"format":"default","field_file_image_alt_text[und][0][value]":"Data Science Bowl Logo","field_file_image_title_text[und][0][value]":"Data Science Bowl Logo","field_folder[und]":"76"},"type":"media","field_deltas":{"1":{"format":"default","field_file_image_alt_text[und][0][value]":"Data Science Bowl

19 CFR 351.303 - Filing, document identification, format, translation, service, and certification of documents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... submit a public version of a database in pdf format. The public version of the database must be publicly... interested party that files with the Department a request for an expedited antidumping review, an..., whichever is later. If the interested party that files the request is unable to locate a particular exporter...

Two graphical user interfaces for managing and analyzing MODFLOW groundwater-model scenarios

USGS Publications Warehouse

Banta, Edward R.

2014-01-01

Scenario Manager and Scenario Analyzer are graphical user interfaces that facilitate the use of calibrated, MODFLOW-based groundwater models for investigating possible responses to proposed stresses on a groundwater system. Scenario Manager allows a user, starting with a calibrated model, to design and run model scenarios by adding or modifying stresses simulated by the model. Scenario Analyzer facilitates the process of extracting data from model output and preparing such display elements as maps, charts, and tables. Both programs are designed for users who are familiar with the science on which groundwater modeling is based but who may not have a groundwater modeler’s expertise in building and calibrating a groundwater model from start to finish. With Scenario Manager, the user can manipulate model input to simulate withdrawal or injection wells, time-variant specified hydraulic heads, recharge, and such surface-water features as rivers and canals. Input for stresses to be simulated comes from user-provided geographic information system files and time-series data files. A Scenario Manager project can contain multiple scenarios and is self-documenting. Scenario Analyzer can be used to analyze output from any MODFLOW-based model; it is not limited to use with scenarios generated by Scenario Manager. Model-simulated values of hydraulic head, drawdown, solute concentration, and cell-by-cell flow rates can be presented in display elements. Map data can be represented as lines of equal value (contours) or as a gradated color fill. Charts and tables display time-series data obtained from output generated by a transient-state model run or from user-provided text files of time-series data. A display element can be based entirely on output of a single model run, or, to facilitate comparison of results of multiple scenarios, an element can be based on output from multiple model runs. Scenario Analyzer can export display elements and supporting metadata as a Portable Document Format file.

47 CFR 1.10008 - What are IBFS file numbers?

Code of Federal Regulations, 2010 CFR

2010-10-01

... Bureau Filing System § 1.10008 What are IBFS file numbers? (a) We assign file numbers to electronic... information, see The International Bureau Filing System File Number Format Public Notice, DA-04-568 (released... 47 Telecommunication 1 2010-10-01 2010-10-01 false What are IBFS file numbers? 1.10008 Section 1...

47 CFR 1.10008 - What are IBFS file numbers?

Code of Federal Regulations, 2011 CFR

2011-10-01

... Bureau Filing System § 1.10008 What are IBFS file numbers? (a) We assign file numbers to electronic... information, see The International Bureau Filing System File Number Format Public Notice, DA-04-568 (released... 47 Telecommunication 1 2011-10-01 2011-10-01 false What are IBFS file numbers? 1.10008 Section 1...

78 FR 30245 - Electric Reliability Organization Interpretation of Specific Requirements of the Disturbance...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-22

... print-to-PDF format and not in a scanned format. Mail/Hand Delivery: Commenters unable to file comments.... FERC, 564 F.3d 1342 (DC Cir. 2009). 3. In March 2007, the Commission issued Order No. 693, evaluating... should be filed in native applications or print-to-PDF format and not in a scanned format. Commenters...

46 CFR 67.218 - Optional filing of instruments in portable document format as attachments to electronic mail.

Code of Federal Regulations, 2010 CFR

2010-10-01

... recording under § 67.200 may be submitted in portable document format (.pdf) as an attachment to electronic... submitted for filing in .pdf format pertains to a vessel that is not a currently documented vessel, a... with the National Vessel Documentation Center or must be submitted in .pdf format with the instrument...

High-Performance, Multi-Node File Copies and Checksums for Clustered File Systems

NASA Technical Reports Server (NTRS)

Kolano, Paul Z.; Ciotti, Robert B.

2012-01-01

Modern parallel file systems achieve high performance using a variety of techniques, such as striping files across multiple disks to increase aggregate I/O bandwidth and spreading disks across multiple servers to increase aggregate interconnect bandwidth. To achieve peak performance from such systems, it is typically necessary to utilize multiple concurrent readers/writers from multiple systems to overcome various singlesystem limitations, such as number of processors and network bandwidth. The standard cp and md5sum tools of GNU coreutils found on every modern Unix/Linux system, however, utilize a single execution thread on a single CPU core of a single system, and hence cannot take full advantage of the increased performance of clustered file systems. Mcp and msum are drop-in replacements for the standard cp and md5sum programs that utilize multiple types of parallelism and other optimizations to achieve maximum copy and checksum performance on clustered file systems. Multi-threading is used to ensure that nodes are kept as busy as possible. Read/write parallelism allows individual operations of a single copy to be overlapped using asynchronous I/O. Multinode cooperation allows different nodes to take part in the same copy/checksum. Split-file processing allows multiple threads to operate concurrently on the same file. Finally, hash trees allow inherently serial checksums to be performed in parallel. Mcp and msum provide significant performance improvements over standard cp and md5sum using multiple types of parallelism and other optimizations. The total speed-ups from all improvements are significant. Mcp improves cp performance over 27x, msum improves md5sum performance almost 19x, and the combination of mcp and msum improves verified copies via cp and md5sum by almost 22x. These improvements come in the form of drop-in replacements for cp and md5sum, so are easily used and are available for download as open source software at http://mutil.sourceforge.net.

NIH Seeks Input on In-patient Clinical Research Areas | Division of Cancer Prevention

Cancer.gov

[[{"fid":"2476","view_mode":"default","fields":{"format":"default","field_file_image_alt_text[und][0][value]":"Aerial view of the National Institutes of Health Clinical Center (Building 10) in Bethesda, Maryland.","field_file_image_title_text[und][0][value]":false},"type":"media","field_deltas":{"1":{"format":"default","field_file_image_alt_text[und][0][value]":"Aerial view of

Pancreatic Cancer Detection Consortium (PCDC) | Division of Cancer Prevention

Cancer.gov

[[{"fid":"2256","view_mode":"default","fields":{"format":"default","field_file_image_alt_text[und][0][value]":"A 3-dimensional image of a human torso highlighting the pancreas.","field_file_image_title_text[und][0][value]":false},"type":"media","field_deltas":{"1":{"format":"default","field_file_image_alt_text[und][0][value]":"A 3-dimensional image of a human torso

Reprocessing of multi-channel seismic-reflection data collected in the Beaufort Sea

USGS Publications Warehouse

Agena, W.F.; Lee, Myung W.; Hart, P.E.

2000-01-01

Contained on this set of two CD-ROMs are stacked and migrated multi-channel seismic-reflection data for 65 lines recorded in the Beaufort Sea by the United States Geological Survey in 1977. All data were reprocessed by the USGS using updated processing methods resulting in improved interpretability. Each of the two CD-ROMs contains the following files: 1) 65 files containing the digital seismic data in standard, SEG-Y format; 2) 1 file containing navigation data for the 65 lines in standard SEG-P1 format; 3) an ASCII text file with cross-reference information for relating the sequential trace numbers on each line to cdp numbers and shotpoint numbers; 4) 2 small scale graphic images (stacked and migrated) of a segment of line 722 in Adobe Acrobat (R) PDF format; 5) a graphic image of the location map, generated from the navigation file; 6) PlotSeis, an MS-DOS Application that allows PC users to interactively view the SEG-Y files; 7) a PlotSeis documentation file; and 8) an explanation of the processing used to create the final seismic sections (this document).

FORMATOMATIC: a program for converting diploid allelic data between common formats for population genetic analysis.

PubMed

Manoukis, Nicholas C

2007-07-01

There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. formatomatic is an easy to use program that can read allelic data files in genepop, raw (csv) or convert formats and create data files in nine formats: raw (csv), arlequin, genepop, immanc/bayesass +, migrate, newhybrids, msvar, baps and structure. Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors.

File formats commonly used in mass spectrometry proteomics.

PubMed

Deutsch, Eric W

2012-12-01

The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to thousands of proteins per experiment. However, the formidable informatics challenge associated with analyzing MS data has required a wide variety of data file formats to encode the complex data types associated with MS workflows. These formats encompass the encoding of input instruction for instruments, output products of the instruments, and several levels of information and results used by and produced by the informatics analysis tools. A brief overview of the most common file formats in use today is presented here, along with a discussion of related topics.

Simple Ontology Format (SOFT)

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

Sorokine, Alexandre

2011-10-01

Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

PubMed

Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

2015-01-01

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

PubMed Central

2012-01-01

Background We present the Biological Observation Matrix (BIOM, pronounced “biome”) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the “ome-ome”) grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. Findings The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. Conclusions The BIOM file format and the biom-format project are steps toward reducing the “bioinformatics bottleneck” that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium. PMID:23587224

76 FR 47606 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-05

... the following formats: One hard copy with original signature, and one electronic copy via e- mail (acceptable file formats are Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or rich text file...

Measles, Mumps, and Rubella (MMR) Vaccination: What Everyone Should Know

MedlinePlus

... rubella combination vaccine Measles=Rubeola Measles=”10-day”, “hard” and “red” measles MMRV=measles, mumps, rubella, and varicella combination vaccine File Formats Help: How do I view different file formats ( ...

A model for a PC-based, universal-format, multimedia digitization system: moving beyond the scanner.

PubMed

McEachen, James C; Cusack, Thomas J; McEachen, John C

2003-08-01

Digitizing images for use in case presentations based on hardcopy films, slides, photographs, negatives, books, and videos can present a challenging task. Scanners and digital cameras have become standard tools of the trade. Unfortunately, use of these devices to digitize multiple images in many different media formats can be a time-consuming and in some cases unachievable process. The authors' goal was to create a PC-based solution for digitizing multiple media formats in a timely fashion while maintaining adequate image presentation quality. The authors' PC-based solution makes use of off-the-shelf hardware applications to include a digital document camera (DDC), VHS video player, and video-editing kit. With the assistance of five staff radiologists, the authors examined the quality of multiple image types digitized with this equipment. The authors also quantified the speed of digitization of various types of media using the DDC and video-editing kit. With regard to image quality, the five staff radiologists rated the digitized angiography, CT, and MR images as adequate to excellent for use in teaching files and case presentations. With regard to digitized plain films, the average rating was adequate. As for performance, the authors recognized a 68% improvement in the time required to digitize hardcopy films using the DDC instead of a professional quality scanner. The PC-based solution provides a means for digitizing multiple images from many different types of media in a timely fashion while maintaining adequate image presentation quality.

Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.

PubMed

Greenwald, William W; Li, He; Smith, Erin N; Benaglio, Paola; Nariai, Naoki; Frazer, Kelly A

2017-04-07

Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite "pgltools": a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.

78 FR 19152 - Revisions to Modeling, Data, and Analysis Reliability Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-29

... processing software should be filed in native applications or print-to-PDF format and not in a scanned format...,126 (2006), aff'd sub nom. Alcoa, Inc. v. FERC, 564 F.3d 1342 (D.C. Cir. 2009). 3. In March 2007, the... print-to-PDF format and not in a scanned format. Commenters filing electronically do not need to make a...

76 FR 75898 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... following formats: One hard copy with original signature, and one electronic copy via email (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Please submit your statement to Douglas Hobbs, Council Coordinator (see FOR FURTHER...

The OpenEarth Framework (OEF) for the 3D Visualization of Integrated Earth Science Data

NASA Astrophysics Data System (ADS)

Nadeau, David; Moreland, John; Baru, Chaitan; Crosby, Chris

2010-05-01

Data integration is increasingly important as we strive to combine data from disparate sources and assemble better models of the complex processes operating at the Earth's surface and within its interior. These data are often large, multi-dimensional, and subject to differing conventions for data structures, file formats, coordinate spaces, and units of measure. When visualized, these data require differing, and sometimes conflicting, conventions for visual representations, dimensionality, symbology, and interaction. All of this makes the visualization of integrated Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data integration and visualization suite of applications and libraries being developed by the GEON project at the University of California, San Diego, USA. Funded by the NSF, the project is leveraging virtual globe technology from NASA's WorldWind to create interactive 3D visualization tools that combine and layer data from a wide variety of sources to create a holistic view of features at, above, and beneath the Earth's surface. The OEF architecture is open, cross-platform, modular, and based upon Java. The OEF's modular approach to software architecture yields an array of mix-and-match software components for assembling custom applications. Available modules support file format handling, web service communications, data management, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats used in the field. Each one imports data into a general-purpose common data model supporting multidimensional regular and irregular grids, topography, feature geometry, and more. Data within these data models may be manipulated, combined, reprojected, and visualized. The OEF's visualization features support a variety of conventional and new visualization techniques for looking at topography, tomography, point clouds, imagery, maps, and feature geometry. 3D data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery, maps, and data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers within a common 3D coordinate space. Data management within the OEF handles and hides the inevitable quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Heuristics are used to extract necessary metadata used to guide data and visual operations. Derived data representations are computed to better support fluid interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization makes use of 3D graphics hardware support found on today's computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

14 CFR 221.195 - Requirement for filing printed material.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (AVIATION PROCEEDINGS) ECONOMIC REGULATIONS TARIFFS Electronically Filed Tariffs § 221.195 Requirement for filing printed material. (a) Any tariff, or revision thereto, filed in paper format which accompanies....190(b). Further, such paper tariff, or revision thereto, shall be filed in accordance with the...

18 CFR 35.7 - Electronic filing requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Electronic filing... § 35.7 Electronic filing requirements. (a) General rule. All filings made in proceedings initiated... declarations or statements and electronic signatures. (c) Format requirements for electronic filing. The...

18 CFR 35.7 - Electronic filing requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Electronic filing... § 35.7 Electronic filing requirements. (a) General rule. All filings made in proceedings initiated... declarations or statements and electronic signatures. (c) Format requirements for electronic filing. The...

18 CFR 35.7 - Electronic filing requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Electronic filing... § 35.7 Electronic filing requirements. (a) General rule. All filings made in proceedings initiated... declarations or statements and electronic signatures. (c) Format requirements for electronic filing. The...

18 CFR 35.7 - Electronic filing requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Electronic filing... § 35.7 Electronic filing requirements. (a) General rule. All filings made in proceedings initiated... declarations or statements and electronic signatures. (c) Format requirements for electronic filing. The...

NIMBUS 7 Earth Radiation Budget (ERB) Matrix User's Guide. Volume 2: Tape Specifications

NASA Technical Reports Server (NTRS)

Ray, S. N.; Vasanth, K. L.

1984-01-01

The ERB MATRIX tape is generated by an IBM 3081 computer program and is a 9 track, 1600 BPI tape. The gross format of the tape given on Page 1, shows an initial standard header file followed by data files. The standard header file contains two standard header records. A trailing documentation file (TDF) is the last file on the tape. Pages 9 through 17 describe, in detail, the standard header file and the TDF. The data files contain data for 37 different ERB parameters. Each file has data based on either a daily, 6 day cyclic, or monthly time interval. There are three types of physical records in the data files; namely, the world grid physical record, the documentation mercator/polar map projection physical record, and the monthly calibration physical record. The manner in which the data for the 37 ERB parameters are stored in the physical records comprising the data files, is given in the gross format section.

Extracting the Data From the LCM vk4 Formatted Output File

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

Wendelberger, James G.

These are slides about extracting the data from the LCM vk4 formatted output file. The following is covered: vk4 file produced by Keyence VK Software, custom analysis, no off the shelf way to read the file, reading the binary data in a vk4 file, various offsets in decimal lines, finding the height image data, directly in MATLAB, binary output beginning of height image data, color image information, color image binary data, color image decimal and binary data, MATLAB code to read vk4 file (choose a file, read the file, compute offsets, read optical image, laser optical image, read and computemore » laser intensity image, read height image, timing, display height image, display laser intensity image, display RGB laser optical images, display RGB optical images, display beginning data and save images to workspace, gamma correction subroutine), reading intensity form the vk4 file, linear in the low range, linear in the high range, gamma correction for vk4 files, computing the gamma intensity correction, observations.« less

Neo: an object model for handling electrophysiology data in multiple formats

PubMed Central

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L.; Rodgers, Chris C.; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P.

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology. PMID:24600386

Neo: an object model for handling electrophysiology data in multiple formats.

PubMed

Garcia, Samuel; Guarino, Domenico; Jaillet, Florent; Jennings, Todd; Pröpper, Robert; Rautenberg, Philipp L; Rodgers, Chris C; Sobolev, Andrey; Wachtler, Thomas; Yger, Pierre; Davison, Andrew P

2014-01-01

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named "Neo," suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.

Five Tips to Help Prevent Infections

MedlinePlus

... Information For… Media Policy Makers 5 Tips to Help Prevent Infections Language: English (US) Español (Spanish) Recommend ... Makers Language: English (US) Español (Spanish) File Formats Help: How do I view different file formats (PDF, ...

ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format.

PubMed

Thomas, Dennis G; Gaheen, Sharon; Harper, Stacey L; Fritts, Martin; Klaessig, Fred; Hahn-Dantona, Elizabeth; Paik, David; Pan, Sue; Stafford, Grace A; Freund, Elaine T; Klemm, Juli D; Baker, Nathan A

2013-01-14

The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials. We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata. The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format

PubMed Central

2013-01-01

Background and motivation The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials. Results We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata. Conclusion The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption. PMID:23311978

77 FR 12108 - Denver & Rio Grande Railway Historical Foundation d/b/a Denver & Rio Grande Railroad, L.L.C...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-28

... via the Board's e-filing format or in the traditional paper format. Any person using e-filing should attach a document and otherwise comply with the instructions at the E-FILING link on the Board's Web site....S.C. 554(e). DRGHF requests that the Board issue an order declaring that municipal zoning law is...

A user-friendly application for the extraction of kubios hrv output to an optimal format for statistical analysis - biomed 2011.

PubMed

Johnsen Lind, Andreas; Helge Johnsen, Bjorn; Hill, Labarron K; Sollers Iii, John J; Thayer, Julian F

2011-01-01

The aim of the present manuscript is to present a user-friendly and flexible platform for transforming Kubios HRV output files to an .xls-file format, used by MS Excel. The program utilizes either native or bundled Java and is platform-independent and mobile. This means that it can run without being installed on a computer. It also has an option of continuous transferring of data indicating that it can run in the background while Kubios produces output files. The program checks for changes in the file structure and automatically updates the .xls- output file.

5 CFR 1201.14 - Electronic filing procedures.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (PDF), and image files (files created by scanning). A list of formats allowed can be found at e-Appeal..., or by uploading the supporting documents in the form of one or more PDF files in which each...

C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes

NASA Astrophysics Data System (ADS)

Rutter, M. J.

2018-04-01

The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used CASTEP [1] electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including CASTEP, ONETEP and VASP, as well as the widely-used 'Gaussian cube' file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes. Data which c2x is capable of extracting from CASTEP's binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats useable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output. C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of CASTEP. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library [2] to report symmetry information, which it can add to .cell files. C2x is a command-line utility, so is readily included in scripts. It is available under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read CASTEP's .check files, so it will have utility in other projects.

Multiple Robots Localization Via Data Sharing

DTIC Science & Technology

2015-09-01

multiple humans, each with specialized skills complementing each other, work to create the solution. Hence, there is a motivation to think in terms of...pygame.Color(255,255,255) COLORBLACK = pygame.Color(0,0,0) F. AUTOMATE.PY The automate.py file is a helper file to assist in running multiple simulation

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

PubMed

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

2009-06-01

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

File Formats Commonly Used in Mass Spectrometry Proteomics*

PubMed Central

Deutsch, Eric W.

2012-01-01

The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to thousands of proteins per experiment. However, the formidable informatics challenge associated with analyzing MS data has required a wide variety of data file formats to encode the complex data types associated with MS workflows. These formats encompass the encoding of input instruction for instruments, output products of the instruments, and several levels of information and results used by and produced by the informatics analysis tools. A brief overview of the most common file formats in use today is presented here, along with a discussion of related topics. PMID:22956731

75 FR 47624 - Sport Fishing and Boating Partnership Council

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-06

... Coordinator in both of the following formats: One hard copy with original signature, and one electronic copy via e- mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). In order to attend this meeting, you must register by...

Performance regression manager for large scale systems

DOEpatents

Faraj, Daniel A.

2017-10-17

System and computer program product to perform an operation comprising generating, based on a first output generated by a first execution instance of a command, a first output file specifying a value of at least one performance metric, wherein the first output file is formatted according to a predefined format, comparing the value of the at least one performance metric in the first output file to a value of the performance metric in a second output file, the second output file having been generated based on a second output generated by a second execution instance of the command, and outputting for display an indication of a result of the comparison of the value of the at least one performance metric of the first output file to the value of the at least one performance metric of the second output file.

Performance regression manager for large scale systems

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

Faraj, Daniel A.

Methods comprising generating, based on a first output generated by a first execution instance of a command, a first output file specifying a value of at least one performance metric, wherein the first output file is formatted according to a predefined format, comparing the value of the at least one performance metric in the first output file to a value of the performance metric in a second output file, the second output file having been generated based on a second output generated by a second execution instance of the command, and outputting for display an indication of a result ofmore » the comparison of the value of the at least one performance metric of the first output file to the value of the at least one performance metric of the second output file.« less

Efficient stereoscopic contents file format on the basis of ISO base media file format

NASA Astrophysics Data System (ADS)

Kim, Kyuheon; Lee, Jangwon; Suh, Doug Young; Park, Gwang Hoon

2009-02-01

A lot of 3D contents haven been widely used for multimedia services, however, real 3D video contents have been adopted for a limited applications such as a specially designed 3D cinema. This is because of the difficulty of capturing real 3D video contents and the limitation of display devices available in a market. However, diverse types of display devices for stereoscopic video contents for real 3D video contents have been recently released in a market. Especially, a mobile phone with a stereoscopic camera has been released in a market, which provides a user as a consumer to have more realistic experiences without glasses, and also, as a content creator to take stereoscopic images or record the stereoscopic video contents. However, a user can only store and display these acquired stereoscopic contents with his/her own devices due to the non-existence of a common file format for these contents. This limitation causes a user not share his/her contents with any other users, which makes it difficult the relevant market to stereoscopic contents is getting expanded. Therefore, this paper proposes the common file format on the basis of ISO base media file format for stereoscopic contents, which enables users to store and exchange pure stereoscopic contents. This technology is also currently under development for an international standard of MPEG as being called as a stereoscopic video application format.

75 FR 5066 - Commission Information Collection Activities (FERC Form 60,1

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-01

... corresponding dockets and collection numbers.) Comments may be filed either electronically or in paper format. Those persons filing electronically do not need to make a paper filing. Documents filed electronically... acknowledgement to the sender's e- mail address upon receipt of comments. For paper filings, the comments should...

Quantitative evaluation of apically extruded debris with different single-file systems: Reciproc, F360 and OneShape versus Mtwo.

PubMed

Bürklein, S; Benten, S; Schäfer, E

2014-05-01

To assess in a laboratory setting the amount of apically extruded debris associated with different single-file nickel-titanium instrumentation systems compared to one multiple-file rotary system. Eighty human mandibular central incisors were randomly assigned to four groups (n = 20 teeth per group). The root canals were instrumented according to the manufacturers' instructions using the reciprocating single-file system Reciproc, the single-file rotary systems F360 and OneShape and the multiple-file rotary Mtwo instruments. The apically extruded debris was collected and dried in pre-weighed glass vials. The amount of debris was assessed with a micro balance and statistically analysed using anova and post hoc Student-Newman-Keuls test. The time required to prepare the canals with the different instruments was also recorded. Reciproc produced significantly more debris compared to all other systems (P < 0.05). No significant difference was noted between the two single-file rotary systems and the multiple-file rotary system (P > 0.05). Instrumentation with the three single-file systems was significantly faster than with Mtwo (P < 0.05). Under the condition of this study, all systems caused apical debris extrusion. Rotary instrumentation was associated with less debris extrusion compared to reciprocal instrumentation. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

PubMed

Bolleman, Jerven T; Mungall, Christopher J; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J P; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; Cock, Peter J A

2016-06-13

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.

NASA-IGES Translator and Viewer

NASA Technical Reports Server (NTRS)

Chou, Jin J.; Logan, Michael A.

1995-01-01

NASA-IGES Translator (NIGEStranslator) is a batch program that translates a general IGES (Initial Graphics Exchange Specification) file to a NASA-IGES-Nurbs-Only (NINO) file. IGES is the most popular geometry exchange standard among Computer Aided Geometric Design (CAD) systems. NINO format is a subset of IGES, implementing the simple and yet the most popular NURBS (Non-Uniform Rational B-Splines) representation. NIGEStranslator converts a complex IGES file to the simpler NINO file to simplify the tasks of CFD grid generation for models in CAD format. The NASA-IGES Viewer (NIGESview) is an Open-Inventor-based, highly interactive viewer/ editor for NINO files. Geometry in the IGES files can be viewed, copied, transformed, deleted, and inquired. Users can use NIGEStranslator to translate IGES files from CAD systems to NINO files. The geometry then can be examined with NIGESview. Extraneous geometries can be interactively removed, and the cleaned model can be written to an IGES file, ready to be used in grid generation.

Transforming clinical imaging and 3D data for virtual reality learning objects: HTML5 and mobile devices implementation.

PubMed

Trelease, Robert B; Nieder, Gary L

2013-01-01

Web deployable anatomical simulations or "virtual reality learning objects" can easily be produced with QuickTime VR software, but their use for online and mobile learning is being limited by the declining support for web browser plug-ins for personal computers and unavailability on popular mobile devices like Apple iPad and Android tablets. This article describes complementary methods for creating comparable, multiplatform VR learning objects in the new HTML5 standard format, circumventing platform-specific limitations imposed by the QuickTime VR multimedia file format. Multiple types or "dimensions" of anatomical information can be embedded in such learning objects, supporting different kinds of online learning applications, including interactive atlases, examination questions, and complex, multi-structure presentations. Such HTML5 VR learning objects are usable on new mobile devices that do not support QuickTime VR, as well as on personal computers. Furthermore, HTML5 VR learning objects can be embedded in "ebook" document files, supporting the development of new types of electronic textbooks on mobile devices that are increasingly popular and self-adopted for mobile learning. © 2012 American Association of Anatomists.

User-programmer dialogue: Guidelines for designing menus and help files for interactive computer systems

NASA Technical Reports Server (NTRS)

Carlson, P. A.

1983-01-01

This document is a set of guidelines to aid a programmer in making the various decisions necessary for a clear user-programmer dialogue. Its goal is to promote an effective and efficient transfer of information between programmer and user. These guidelines are divided into four sections: (1) Format, (2) Sequence, (3) Audience, and (4) Aim. Format, in terms of this study, means the spatial and structural presentation of information. Sequence deals with the procedural aspects of multiple panel displays. This section looks at the issues of timelines of presentation, modularization of information, and patterns of user behavior. Audience looks at the relationship among programmer, user, and message. It covers the issues of analyzing the audience's knowledge, attitudes, and needs, anticipating the audience's inferences, and identifying textual ambiguities. The programmer's aim or intention shows up in everything from tone to format. Aim considers the programmer's purpose.

[Intranet-based integrated information system of radiotherapy-related images and diagnostic reports].

PubMed

Nakamura, R; Sasaki, M; Oikawa, H; Harada, S; Tamakawa, Y

2000-03-01

To use an intranet technique to develop an information system that simultaneously supports both diagnostic reports and radiotherapy planning images. Using a file server as the gateway a radiation oncology LAN was connected to an already operative RIS LAN. Dose-distribution images were saved in tagged-image-file format by way of a screen dump to the file server. X-ray simulator images and portal images were saved in encapsulated postscript format in the file server and automatically converted to portable document format. The files on the file server were automatically registered to the Web server by the search engine and were available for searching and browsing using the Web browser. It took less than a minute to register planning images. For clients, searching and browsing the file took less than 3 seconds. Over 150,000 reports and 4,000 images from a six-month period were accessible. Because the intranet technique was used, construction and maintenance was completed without specialty. Prompt access to essential information about radiotherapy has been made possible by this system. It promotes public access to radiotherapy planning that may improve the quality of treatment.

77 FR 60138 - Trinity Adaptive Management Working Group; Public Teleconference/Web-Based Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-02

... statements must be supplied to Elizabeth Hadley in one of the following formats: One hard copy with original... file formats are Adobe Acrobat PDF, MS Word, PowerPoint, or rich text file). Registered speakers who...

E-submission chronic toxicology study supplemental files

EPA Pesticide Factsheets

The formats and instructions in these documents are designed to be used as an example or guide for registrants to format electronic files for submission of animal toxicology data to OPP for review in support of registration and reevaluation of pesticides.

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

PubMed

Bradley, Anthony R; Rose, Alexander S; Pavelka, Antonín; Valasatava, Yana; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

2017-06-01

Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.

MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

PubMed Central

Pavelka, Antonín; Valasatava, Yana; Prlić, Andreas

2017-01-01

Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis. PMID:28574982

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

PubMed

Karthikeyan, Muthukumarasamy; Vyas, Renu

2016-01-01

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

MESHMAKER (MM) V1.5

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

MORIDIS, GEORGE

2016-05-02

MeshMaker v1.5 is a code that describes the system geometry and discretizes the domain in problems of flow and transport through porous and fractured media that are simulated using the TOUGH+ [Moridis and Pruess, 2014] or TOUGH2 [Pruess et al., 1999; 2012] families of codes. It is a significantly modified and drastically enhanced version of an earlier simpler facility that was embedded in the TOUGH2 codes [Pruess et al., 1999; 2012], from which it could not be separated. The code (MeshMaker.f90) is a stand-alone product written in FORTRAN 95/2003, is written according to the tenets of Object-Oriented Programming, has amore » modular structure and can perform a number of mesh generation and processing operations. It can generate two-dimensional radially symmetric (r,z) meshes, and one-, two-, and three-dimensional rectilinear (Cartesian) grids in (x,y,z). The code generates the file MESH, which includes all the elements and connections that describe the discretized simulation domain and conforming to the requirements of the TOUGH+ and TOUGH2 codes. Multiple-porosity processing for simulation of flow in naturally fractured reservoirs can be invoked by means of a keyword MINC, which stands for Multiple INteracting Continua. The MINC process operates on the data of the primary (porous medium) mesh as provided on disk file MESH, and generates a secondary mesh containing fracture and matrix elements with identical data formats on file MINC.« less

CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules.

PubMed

Aguirre-Valderrama, Alonso; Dobado, José A

2008-12-01

Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.

MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra.

PubMed

Kim, Sangtae; Na, Seungjin; Sim, Ji Woong; Park, Heejin; Jeong, Jaeho; Kim, Hokeun; Seo, Younghwan; Seo, Jawon; Lee, Kong-Joo; Paek, Eunok

2006-07-01

MOD(i) (http://modi.uos.ac.kr/modi/) is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MOD(i), one can consider for analysis both the entire PTM list published on the unimod webpage (http://www.unimod.org) and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MOD(i) is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MOD(i)'s output in a user-friendly manner and helps users understand MOD(i)'s output quickly. In addition, one can perform manual de novo sequencing using MassPective.

Network Configuration Analysis for Formation Flying Satellites

NASA Technical Reports Server (NTRS)

Knoblock, Eric J.; Wallett, Thomas M.; Konangi, Vijay K.; Bhasin, Kul B.

2001-01-01

The performance of two networks to support autonomous multi-spacecraft formation flying systems is presented. Both systems are comprised of a ten-satellite formation, with one of the satellites designated as the central or 'mother ship.' All data is routed through the mother ship to the terrestrial network. The first system uses a TCP/EP over ATM protocol architecture within the formation, and the second system uses the IEEE 802.11 protocol architecture within the formation. The simulations consist of file transfers using either the File Transfer Protocol (FTP) or the Simple Automatic File Exchange (SAFE) Protocol. The results compare the IP queuing delay, IP queue size and IP processing delay at the mother ship as well as end-to-end delay for both systems. In all cases, using IEEE 802.11 within the formation yields less delay. Also, the throughput exhibited by SAFE is better than FTP.

A collection of public transport network data sets for 25 cities

PubMed Central

Kujala, Rainer; Weckström, Christoffer; Darst, Richard K.; Mladenović, Miloš N; Saramäki, Jari

2018-01-01

Various public transport (PT) agencies publish their route and timetable information with the General Transit Feed Specification (GTFS) as the standard open format. Timetable data are commonly used for PT passenger routing. They can also be used for studying the structure and organization of PT networks, as well as the accessibility and the level of service these networks provide. However, using raw GTFS data is challenging as researchers need to understand the details of the GTFS data format, make sure that the data contain all relevant modes of public transport, and have no errors. To lower the barrier for using GTFS data in research, we publish a curated collection of 25 cities' public transport networks in multiple easy-to-use formats including network edge lists, temporal network event lists, SQLite databases, GeoJSON files, and the GTFS data format. This collection promotes the study of how PT is organized across the globe, and also provides a testbed for developing tools for PT network analysis and PT routing algorithms. PMID:29762553

Format( )MEDIC( )Input

NASA Astrophysics Data System (ADS)

Foster, K.

1994-09-01

This document is a description of a computer program called Format( )MEDIC( )Input. The purpose of this program is to allow the user to quickly reformat wind velocity data in the Model Evaluation Database (MEDb) into a reasonable 'first cut' set of MEDIC input files (MEDIC.nml, StnLoc.Met, and Observ.Met). The user is cautioned that these resulting input files must be reviewed for correctness and completeness. This program will not format MEDb data into a Problem Station Library or Problem Metdata File. A description of how the program reformats the data is provided, along with a description of the required and optional user input and a description of the resulting output files. A description of the MEDb is not provided here but can be found in the RAS Division Model Evaluation Database Description document.

77 FR 66830 - LNG Development Company, LLC and Oregon Pipeline Company; Northwest Pipeline GP; Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-07

... can file your comments electronically using the eFiling feature located on the Commission's Web site ( www.ferc.gov ) under the Documents & Filings link. With eFiling, you can provide comments in a variety of formats by attaching them as a file with your submission. New eFiling users must first create an...

76 FR 32198 - Science Advisory Board Staff Office Notification of a Joint Public Meeting of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-03

... meeting. Written statements should be supplied to the DFO in the following formats: One hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, MS Word, WordPerfect, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are...

76 FR 4346 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-25

... their consideration. Written statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format...

75 FR 4816 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

... statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to provide...

75 FR 52940 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Chartered Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-30

... should be supplied to the DFO in the following formats: One hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, MS Word, WordPerfect, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to provide electronic...

75 FR 80048 - Science Advisory Board Staff Office; Notification of an Upcoming Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-21

... be supplied to the DFO in the following formats: One hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format). Submitters are requested to provide two...

75 FR 37793 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-30

... supplied to the DFO in the following formats: One hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format). Submitters are requested to provide two versions...

75 FR 1381 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Clean Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-11

... supplied to the DFO in the following formats: one hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, MS Word, WordPerfect, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to provide versions of each...

76 FR 16769 - Science Advisory Board Staff Office; Notification of a Public Meeting of the Science Advisory...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-25

... statements should be supplied to the DFO in the following formats: One hard copy with original signature and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are requested to provide...

75 FR 62386 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-08

.... Written statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/Windows 98/2000/XP format). Submitters are asked to...

76 FR 11245 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-01

... their consideration. Written statements should be supplied to the DFO in the following formats: one hard copy with original signature, and one electronic copy via e-mail (acceptable file format: Adobe Acrobat PDF, WordPerfect, MS Word, MS PowerPoint, or Rich Text files in IBM-PC/ Windows 98/2000/XP format...

Regional seismic lines reprocessed using post-stack processing techniques; National Petroleum Reserve, Alaska

USGS Publications Warehouse

Miller, John J.; Agena, W.F.; Lee, M.W.; Zihlman, F.N.; Grow, J.A.; Taylor, D.J.; Killgore, Michele; Oliver, H.L.

2000-01-01

This CD-ROM contains stacked, migrated, 2-Dimensional seismic reflection data and associated support information for 22 regional seismic lines (3,470 line-miles) recorded in the National Petroleum Reserve ? Alaska (NPRA) from 1974 through 1981. Together, these lines constitute about one-quarter of the seismic data collected as part of the Federal Government?s program to evaluate the petroleum potential of the Reserve. The regional lines, which form a grid covering the entire NPRA, were created by combining various individual lines recorded in different years using different recording parameters. These data were reprocessed by the USGS using modern, post-stack processing techniques, to create a data set suitable for interpretation on interactive seismic interpretation computer workstations. Reprocessing was done in support of ongoing petroleum resource studies by the USGS Energy Program. The CD-ROM contains the following files: 1) 22 files containing the digital seismic data in standard, SEG-Y format; 2) 1 file containing navigation data for the 22 lines in standard SEG-P1 format; 3) 22 small scale graphic images of each seismic line in Adobe Acrobat? PDF format; 4) a graphic image of the location map, generated from the navigation file, with hyperlinks to the graphic images of the seismic lines; 5) an ASCII text file with cross-reference information for relating the sequential trace numbers on each regional line to the line number and shotpoint number of the original component lines; and 6) an explanation of the processing used to create the final seismic sections (this document). The SEG-Y format seismic files and SEG-P1 format navigation file contain all the information necessary for loading the data onto a seismic interpretation workstation.

17 CFR 232.14 - Paper filings not accepted without exemption.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 17 Commodity and Securities Exchanges 2 2011-04-01 2011-04-01 false Paper filings not accepted... COMMISSION REGULATION S-T-GENERAL RULES AND REGULATIONS FOR ELECTRONIC FILINGS General § 232.14 Paper filings not accepted without exemption. The Commission will not accept in paper format any filing required to...

Earth Science Datacasting v2.0

NASA Technical Reports Server (NTRS)

Bingham, Andrew W.; Deen, Robert G.; Hussey, Kevin J.; Stough, Timothy M.; McCleese, Sean W.; Toole, Nicholas T.

2012-01-01

The Datacasting software, which consists of a server and a client, has been developed as part of the Earth Science (ES) Datacasting project. The goal of ES Datacasting is to provide scientists the ability to automatically and continuously download Earth science data that meets a precise, predefined need, and then to instantaneously visualize it on a local computer. This is achieved by applying the concept of podcasting to deliver science data over the Internet using RSS (Really Simple Syndication) XML feeds. By extending the RSS specification, scientists can filter a feed and only download the files that are required for a particular application (for example, only files that contain information about a particular event, such as a hurricane or flood). The extension also provides the ability for the client to understand the format of the data and visualize the information locally. The server part enables a data provider to create and serve basic Datacasting (RSS-based) feeds. The user can subscribe to any number of feeds, view the information related to each item contained within a feed (including browse pre-made images), manually download files associated with items, and place these files in a local store. The client-server architecture enables users to: a) Subscribe and interpret multiple Datacasting feeds (same look and feel as a typical mail client), b) Maintain a list of all items within each feed, c) Enable filtering on the lists based on different metadata attributes contained within the feed (list will reference only data files of interest), d) Visualize the reference data and associated metadata, e) Download files referenced within the list, and f) Automatically download files as new items become available.

UAEMIAAE

Atmospheric Science Data Center

2013-12-19

UAEMIAAE Aerosol product. ( File version details ) File version  F07_0015  has better ... properties. File version  F08_0016  has improved cloud screening procedure resulting in better aerosol optical depth. ... Coverage:  August - October 2004 File Format:  HDF-EOS Tools:  FTP Access: Data Pool ...

Performance regression manager for large scale systems

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

Faraj, Daniel A.

System and computer program product to perform an operation comprising generating, based on a first output generated by a first execution instance of a command, a first output file specifying a value of at least one performance metric, wherein the first output file is formatted according to a predefined format, comparing the value of the at least one performance metric in the first output file to a value of the performance metric in a second output file, the second output file having been generated based on a second output generated by a second execution instance of the command, and outputtingmore » for display an indication of a result of the comparison of the value of the at least one performance metric of the first output file to the value of the at least one performance metric of the second output file.« less

Visualization of seismic tomography on Google Earth: Improvement of KML generator and its web application to accept the data file in European standard format

NASA Astrophysics Data System (ADS)

Yamagishi, Y.; Yanaka, H.; Tsuboi, S.

2009-12-01

We have developed a conversion tool for the data of seismic tomography into KML, called KML generator, and made it available on the web site (http://www.jamstec.go.jp/pacific21/google_earth). The KML generator enables us to display vertical and horizontal cross sections of the model on Google Earth in three-dimensional manner, which would be useful to understand the Earth's interior. The previous generator accepts text files of grid-point data having longitude, latitude, and seismic velocity anomaly. Each data file contains the data for each depth. Metadata, such as bibliographic reference, grid-point interval, depth, are described in other information file. We did not allow users to upload their own tomographic model to the web application, because there is not standard format to represent tomographic model. Recently European seismology research project, NEIRES (Network of Research Infrastructures for European Seismology), advocates that the data of seismic tomography should be standardized. They propose a new format based on JSON (JavaScript Object Notation), which is one of the data-interchange formats, as a standard one for the tomography. This format consists of two parts, which are metadata and grid-point data values. The JSON format seems to be powerful to handle and to analyze the tomographic model, because the structure of the format is fully defined by JavaScript objects, thus the elements are directly accessible by a script. In addition, there exist JSON libraries for several programming languages. The International Federation of Digital Seismograph Network (FDSN) adapted this format as a FDSN standard format for seismic tomographic model. There might be a possibility that this format would not only be accepted by European seismologists but also be accepted as the world standard. Therefore we improve our KML generator for seismic tomography to accept the data file having also JSON format. We also improve the web application of the generator so that the JSON formatted data file can be uploaded. Users can convert any tomographic model data to KML. The KML obtained through the new generator should provide an arena to compare various tomographic models and other geophysical observations on Google Earth, which may act as a common platform for geoscience browser.

The Galley Parallel File System

NASA Technical Reports Server (NTRS)

Nieuwejaar, Nils; Kotz, David

1996-01-01

As the I/O needs of parallel scientific applications increase, file systems for multiprocessors are being designed to provide applications with parallel access to multiple disks. Many parallel file systems present applications with a conventional Unix-like interface that allows the application to access multiple disks transparently. The interface conceals the parallelism within the file system, which increases the ease of programmability, but makes it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. Furthermore, most current parallel file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic parallel workloads. We discuss Galley's file structure and application interface, as well as an application that has been implemented using that interface.

National Geochemical Database reformatted data from the National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) program

USGS Publications Warehouse

Smith, Steven M.

1997-01-01

The National Uranium Resource Evaluation (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) program produced a large amount of geochemical data. To fully understand how these data were generated, it is recommended that you read the History of NURE HSSR Program for a summary of the entire program. By the time the NURE program had ended, the HSSR data consisted of 894 separate data files stored with 47 different formats. Many files contained duplication of data found in other files. The University of Oklahoma's Information Systems Programs of the Energy Resources Institute (ISP) was contracted by the Department of Energy to enhance the accessibility and usefulness of the NURE HSSR data. ISP created a single standard-format master file to replace the 894 original files. ISP converted 817 of the 894 original files before its funding apparently ran out. The ISP-reformatted NURE data files have been released by the USGS on CD-ROM (Lower 48 States, Hoffman and Buttleman, 1994; Alaska, Hoffman and Buttleman, 1996). A description of each NURE database field, derived from a draft NURE HSSR data format manual (unpubl. commun., Stan Moll, ISP, Oct 7, 1988), was included in a readme file on each CD-ROM. That original manual was incomplete and assumed that the reformatting process had gone to completion. A lot of vital information was not included. Efforts to correct that manual and the NURE data revealed a large number of problems and missing data. As a result of the frustrating process of cleaning and re-cleaning data from the ISP-reformatted NURE files, a new NURE HSSR data format was developed. This work represents a totally new attempt to reformat the original NURE files into 2 consistent database structures; one for water samples and a second for sediment samples, on a quadrangle by quadrangle basis, from the original NURE files. Although this USGS-reformatted NURE HSSR data format is different than that created by the ISP, many of their ideas were incorporated and expanded in this effort. All of the data from each quadrangle are being examined thoroughly in an attempt to eliminate problems, to combine partial or duplicate records, to convert all coding to a common scheme, and to identify problems even if they can not be solved at this time.

Development of the Large-Scale Statistical Analysis System of Satellites Observations Data with Grid Datafarm Architecture

NASA Astrophysics Data System (ADS)

Yamamoto, K.; Murata, K.; Kimura, E.; Honda, R.

2006-12-01

In the Solar-Terrestrial Physics (STP) field, the amount of satellite observation data has been increasing every year. It is necessary to solve the following three problems to achieve large-scale statistical analyses of plenty of data. (i) More CPU power and larger memory and disk size are required. However, total powers of personal computers are not enough to analyze such amount of data. Super-computers provide a high performance CPU and rich memory area, but they are usually separated from the Internet or connected only for the purpose of programming or data file transfer. (ii) Most of the observation data files are managed at distributed data sites over the Internet. Users have to know where the data files are located. (iii) Since no common data format in the STP field is available now, users have to prepare reading program for each data by themselves. To overcome the problems (i) and (ii), we constructed a parallel and distributed data analysis environment based on the Gfarm reference implementation of the Grid Datafarm architecture. The Gfarm shares both computational resources and perform parallel distributed processings. In addition, the Gfarm provides the Gfarm filesystem which can be as virtual directory tree among nodes. The Gfarm environment is composed of three parts; a metadata server to manage distributed files information, filesystem nodes to provide computational resources and a client to throw a job into metadata server and manages data processing schedulings. In the present study, both data files and data processes are parallelized on the Gfarm with 6 file system nodes: CPU clock frequency of each node is Pentium V 1GHz, 256MB memory and40GB disk. To evaluate performances of the present Gfarm system, we scanned plenty of data files, the size of which is about 300MB for each, in three processing methods: sequential processing in one node, sequential processing by each node and parallel processing by each node. As a result, in comparison between the number of files and the elapsed time, parallel and distributed processing shorten the elapsed time to 1/5 than sequential processing. On the other hand, sequential processing times were shortened in another experiment, whose file size is smaller than 100KB. In this case, the elapsed time to scan one file is within one second. It implies that disk swap took place in case of parallel processing by each node. We note that the operation became unstable when the number of the files exceeded 1000. To overcome the problem (iii), we developed an original data class. This class supports our reading of data files with various data formats since it converts them into an original data format since it defines schemata for every type of data and encapsulates the structure of data files. In addition, since this class provides a function of time re-sampling, users can easily convert multiple data (array) with different time resolution into the same time resolution array. Finally, using the Gfarm, we achieved a high performance environment for large-scale statistical data analyses. It should be noted that the present method is effective only when one data file size is large enough. At present, we are restructuring the new Gfarm environment with 8 nodes: CPU is Athlon 64 x2 Dual Core 2GHz, 2GB memory and 1.2TB disk (using RAID0) for each node. Our original class is to be implemented on the new Gfarm environment. In the present talk, we show the latest results with applying the present system for data analyses with huge number of satellite observation data files.

Effect of reciprocating file motion on microcrack formation in root canals: an SEM study.

PubMed

Ashwinkumar, V; Krithikadatta, J; Surendran, S; Velmurugan, N

2014-07-01

To compare dentinal microcrack formation whilst using Ni-Ti hand K-files, ProTaper hand and rotary files and the WaveOne reciprocating file. One hundred and fifty mandibular first molars were selected. Thirty teeth were left unprepared and served as controls, and the remaining 120 teeth were divided into four groups. Ni-Ti hand K-files, ProTaper hand files, ProTaper rotary files and WaveOne Primary reciprocating files were used to prepare the mesial canals. Roots were then sectioned 3, 6 and 9 mm from the apex, and the cut surface was observed under scanning electron microscope (SEM) and checked for the presence of dentinal microcracks. The control and Ni-Ti hand K-files groups were not associated with microcracks. In roots prepared with ProTaper hand files, ProTaper rotary files and WaveOne Primary reciprocating files, dentinal microcracks were present. There was a significant difference between control/Ni-Ti hand K-files group and ProTaper hand files/ProTaper rotary files/WaveOne Primary reciprocating file group (P < 0.001) with ProTaper rotary files producing the most microcracks. No significant difference was observed between teeth prepared with ProTaper hand files and WaveOne Primary reciprocating files. ProTaper rotary files were associated with significantly more microcracks than ProTaper hand files and WaveOne Primary reciprocating files. Ni-Ti hand K-files did not produce microcracks at any levels inside the root canals. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

A heterobimetallic complex featuring a Ti–Co multiple bond and its application to the reductive coupling of ketones to alkenes† †Electronic supplementary information (ESI) available: Experimental procedures, additional spectroscopic data for 1–4, and computational details of 2 and 3. CCDC 1037714–1037716. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03772c Click here for additional data file. Click here for additional data file.

PubMed Central

Wu, Bing; Bezpalko, Mark W.; Foxman, Bruce M.

2015-01-01

To explore metal–metal multiple bonds between first row transition metals, Ti/Co complexes supported by two phosphinoamide ligands have been synthesized and characterized. The Ti metalloligand Cl2Ti(XylNPiPr2)2 (1) was treated with CoI2 under reducing conditions, permitting isolation of the Ti/Co complex [(μ-Cl)Ti(XylNPiPr2)2CoI]2 (2). One electron reduction of complex 2 affords ClTi(XylNPiPr2)2CoPMe3 (3), which features a metal–metal triple bond and an unprecedentedly short Ti–Co distance of 2.0236(9) Å. This complex is shown to promote the McMurry coupling reaction of aryl ketones into alkenes, with concomitant formation of the tetranuclear complex [Ti(μ3-O)(NXylPiPr2)2CoI]2 (4). A cooperative mechanism involving bimetallic C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 O bond activation and a cobalt carbene intermediate is proposed. PMID:29142672

DICOM to print, 35-mm slides, web, and video projector: tutorial using Adobe Photoshop.

PubMed

Gurney, Jud W

2002-10-01

Preparing images for publication has dealt with film and the photographic process. With picture archiving and communications systems, many departments will no longer produce film. This will change how images are produced for publication. DICOM, the file format for radiographic images, has to be converted and then prepared for traditional publication, 35-mm slides, the newest techniques of video projection, and the World Wide Web. Tagged image file format is the common format for traditional print publication, whereas joint photographic expert group is the current file format for the World Wide Web. Each medium has specific requirements that can be met with a common image-editing program such as Adobe Photoshop (Adobe Systems, San Jose, CA). High-resolution images are required for print, a process that requires interpolation. However, the Internet requires images with a small file size for rapid transmission. The resolution of each output differs and the image resolution must be optimized to match the output of the publishing medium.

TADPLOT program, version 2.0: User's guide

NASA Technical Reports Server (NTRS)

Hammond, Dana P.

1991-01-01

The TADPLOT Program, Version 2.0 is described. The TADPLOT program is a software package coordinated by a single, easy-to-use interface, enabling the researcher to access several standard file formats, selectively collect specific subsets of data, and create full-featured publication and viewgraph quality plots. The user-interface was designed to be independent from any file format, yet provide capabilities to accommodate highly specialized data queries. Integrated with an applications software network, data can be assessed, collected, and viewed quickly and easily. Since the commands are data independent, subsequent modifications to the file format will be transparent, while additional file formats can be integrated with minimal impact on the user-interface. The graphical capabilities are independent of the method of data collection; thus, the data specification and subsequent plotting can be modified and upgraded as separate functional components. The graphics kernel selected adheres to the full functional specifications of the CORE standard. Both interface and postprocessing capabilities are fully integrated into TADPLOT.

Converting CSV Files to RKSML Files

NASA Technical Reports Server (NTRS)

Trebi-Ollennu, Ashitey; Liebersbach, Robert

2009-01-01

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

Fortran Program for X-Ray Photoelectron Spectroscopy Data Reformatting

NASA Technical Reports Server (NTRS)

Abel, Phillip B.

1989-01-01

A FORTRAN program has been written for use on an IBM PC/XT or AT or compatible microcomputer (personal computer, PC) that converts a column of ASCII-format numbers into a binary-format file suitable for interactive analysis on a Digital Equipment Corporation (DEC) computer running the VGS-5000 Enhanced Data Processing (EDP) software package. The incompatible floating-point number representations of the two computers were compared, and a subroutine was created to correctly store floating-point numbers on the IBM PC, which can be directly read by the DEC computer. Any file transfer protocol having provision for binary data can be used to transmit the resulting file from the PC to the DEC machine. The data file header required by the EDP programs for an x ray photoelectron spectrum is also written to the file. The user is prompted for the relevant experimental parameters, which are then properly coded into the format used internally by all of the VGS-5000 series EDP packages.

The effect of multiple autoclave cycles on the surface of rotary nickel-titanium endodontic files: An in vitro atomic force microscopy investigation

PubMed Central

Nair, Ashish Shashikant; Tilakchand, Mahima; Naik, Balaram Damodar

2015-01-01

Aims: To observe and study the effect of multiple autoclave sterilization cycles, on the surface of nickel-titanium (NiTi) files. Materials and Methods: The file used for this study was the Mtwo file (VDW) and ProTaper (Dentsply). The apical 5 mm of the files were attached to a silicon wafer and subjected to autoclave cycles under standardized conditions. They were scanned with an AFM after 1, 5, and 10 cycles. The unsterilized files were used as control, before start of the study. Three vertical topographic parameters namely maximum height (MH), root mean square (RMS) of surface roughness, and arithmetic mean roughness (AMR)were measured with the atomic force microscope (AFM). Analysis of variance along with Tukey's test was used to test the differences. Results: The vertical topographic parameters were higher for both the files, right after the first cycle, when compared with the control (P < 0.01). The surface roughness increased sharply for Mtwo when compared to ProTaper, though ProTaper had a rougher surface initially. Conclusions: The study confirmed that the irregularities present on the surface of the file became more prominent with multiple autoclave cycles, a fact that should be kept in mind during their reuse. PMID:26069408

The effect of multiple autoclave cycles on the surface of rotary nickel-titanium endodontic files: An in vitro atomic force microscopy investigation.

PubMed

Nair, Ashish Shashikant; Tilakchand, Mahima; Naik, Balaram Damodar

2015-01-01

To observe and study the effect of multiple autoclave sterilization cycles, on the surface of nickel-titanium (NiTi) files. The file used for this study was the Mtwo file (VDW) and ProTaper (Dentsply). The apical 5 mm of the files were attached to a silicon wafer and subjected to autoclave cycles under standardized conditions. They were scanned with an AFM after 1, 5, and 10 cycles. The unsterilized files were used as control, before start of the study. Three vertical topographic parameters namely maximum height (MH), root mean square (RMS) of surface roughness, and arithmetic mean roughness (AMR)were measured with the atomic force microscope (AFM). Analysis of variance along with Tukey's test was used to test the differences. The vertical topographic parameters were higher for both the files, right after the first cycle, when compared with the control (P < 0.01). The surface roughness increased sharply for Mtwo when compared to ProTaper, though ProTaper had a rougher surface initially. The study confirmed that the irregularities present on the surface of the file became more prominent with multiple autoclave cycles, a fact that should be kept in mind during their reuse.

78 FR 6319 - Notice of Availability of the Report: Recommended Parameters for Solid Flame Models for Land...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-30

... file your comments electronically using the eFiling feature on the Commission's Web site ( www.ferc.gov ) under the link to Documents and Filings. With eFiling, you can provide comments in a variety of formats by attaching them as a file with your submission. New eFiling users must first create an account by...

77 FR 53885 - Jordan Cove Energy Project LP, Pacific Connector Gas Pipeline LP; Notice of Extension of Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-04

... on a project; (2) You can file your comments electronically using the eFiling feature located on the Commission's Web site ( www.ferc.gov ) under the Documents & Filings link. With eFiling, you can provide comments in a variety of formats by attaching them as a file with your submission. New eFiling users must...

A convertor and user interface to import CAD files into worldtoolkit virtual reality systems

NASA Technical Reports Server (NTRS)

Wang, Peter Hor-Ching

1996-01-01

Virtual Reality (VR) is a rapidly developing human-to-computer interface technology. VR can be considered as a three-dimensional computer-generated Virtual World (VW) which can sense particular aspects of a user's behavior, allow the user to manipulate the objects interactively, and render the VW at real-time accordingly. The user is totally immersed in the virtual world and feel the sense of transforming into that VW. NASA/MSFC Computer Application Virtual Environments (CAVE) has been developing the space-related VR applications since 1990. The VR systems in CAVE lab are based on VPL RB2 system which consists of a VPL RB2 control tower, an LX eyephone, an Isotrak polhemus sensor, two Fastrak polhemus sensors, a folk of Bird sensor, and two VPL DG2 DataGloves. A dynamics animator called Body Electric from VPL is used as the control system to interface with all the input/output devices and to provide the network communications as well as VR programming environment. The RB2 Swivel 3D is used as the modelling program to construct the VW's. A severe limitation of the VPL VR system is the use of RB2 Swivel 3D, which restricts the files to a maximum of 1020 objects and doesn't have the advanced graphics texture mapping. The other limitation is that the VPL VR system is a turn-key system which does not provide the flexibility for user to add new sensors and C language interface. Recently, NASA/MSFC CAVE lab provides VR systems built on Sense8 WorldToolKit (WTK) which is a C library for creating VR development environments. WTK provides device drivers for most of the sensors and eyephones available on the VR market. WTK accepts several CAD file formats, such as Sense8 Neutral File Format, AutoCAD DXF and 3D Studio file format, Wave Front OBJ file format, VideoScape GEO file format, Intergraph EMS stereolithographics and CATIA Stereolithographics STL file formats. WTK functions are object-oriented in their naming convention, are grouped into classes, and provide easy C language interface. Using a CAD or modelling program to build a VW for WTK VR applications, we typically construct the stationary universe with all the geometric objects except the dynamic objects, and create each dynamic object in an individual file.

Using GDAL to Convert NetCDF 4 CF 1.6 to GeoTIFF: Interoperability Problems and Solutions for Data Providers and Distributors

NASA Astrophysics Data System (ADS)

Haran, T. M.; Brodzik, M. J.; Nordgren, B.; Estilow, T.; Scott, D. J.

2015-12-01

An increasing number of new Earth science datasets are being producedby data providers in self-describing, machine-independent file formatsincluding Hierarchical Data Format version 5 (HDF5) and NetworkCommon Data Form version 4 (netCDF-4). Furthermore data providers maybe producing netCDF-4 files that follow the conventions for Climateand Forecast metadata version 1.6 (CF 1.6) which, for datasets mappedto a projected raster grid covering all or a portion of the earth,includes the Coordinate Reference System (CRS) used to define howlatitude and longitude are mapped to grid coordinates, i.e. columnsand rows, and vice versa. One problem that users may encounter is thattheir preferred visualization and analysis tool may not yet includesupport for one of these newer formats. Moreover, data distributorssuch as NASA's NSIDC DAAC may not yet include support for on-the-flyconversion of data files for all data sets produced in a new format toa preferred older distributed format.There do exist open source solutions to this dilemma in the form ofsoftware packages that can translate files in one of the new formatsto one of the preferred formats. However these software packagesrequire that the file to be translated conform to the specificationsof its respective format. Although an online CF-Convention compliancechecker is available from cfconventions.org, a recent NSIDC userservices incident described here in detail involved an NSIDC-supporteddata set that passed the (then current) CF Checker Version 2.0.6, butwas in fact lacking two variables necessary for conformance. Thisproblem was not detected until GDAL, a software package which reliedon the missing variables, was employed by a user in an attempt totranslate the data into a different file format, namely GeoTIFF.This incident indicates that testing a candidate data product with oneor more software products written to accept the advertised conventionsis proposed as a practice which improves interoperability. Differencesbetween data file contents and software package expectations areexposed, affording an opportunity to improve conformance of software,data or both. The incident can also serve as a demonstration that dataproviders, distributors, and users can work together to improve dataproduct quality and interoperability.

MrEnt: an editor for publication-quality phylogenetic tree illustrations.

PubMed

Zuccon, Alessandro; Zuccon, Dario

2014-09-01

We developed MrEnt, a Windows-based, user-friendly software that allows the production of complex, high-resolution, publication-quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication. © 2014 John Wiley & Sons Ltd.

41 CFR 301-52.3 - Am I required to file a travel claim in a specific format and must the claim be signed?

Code of Federal Regulations, 2010 CFR

2010-07-01

... that time, you must file your travel claim in the format prescribed by your agency. If the prescribed... travel claim in a specific format and must the claim be signed? 301-52.3 Section 301-52.3 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES...

41 CFR 301-52.3 - Am I required to file a travel claim in a specific format and must the claim be signed?

Code of Federal Regulations, 2013 CFR

2013-07-01

... that time, you must file your travel claim in the format prescribed by your agency. If the prescribed... travel claim in a specific format and must the claim be signed? 301-52.3 Section 301-52.3 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES...

41 CFR 301-52.3 - Am I required to file a travel claim in a specific format and must the claim be signed?

Code of Federal Regulations, 2011 CFR

2011-07-01

... that time, you must file your travel claim in the format prescribed by your agency. If the prescribed... travel claim in a specific format and must the claim be signed? 301-52.3 Section 301-52.3 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES...

41 CFR 301-52.3 - Am I required to file a travel claim in a specific format and must the claim be signed?

Code of Federal Regulations, 2014 CFR

2014-07-01

... that time, you must file your travel claim in the format prescribed by your agency. If the prescribed... travel claim in a specific format and must the claim be signed? 301-52.3 Section 301-52.3 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES...

41 CFR 301-52.3 - Am I required to file a travel claim in a specific format and must the claim be signed?

Code of Federal Regulations, 2012 CFR

2012-07-01

... that time, you must file your travel claim in the format prescribed by your agency. If the prescribed... travel claim in a specific format and must the claim be signed? 301-52.3 Section 301-52.3 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES...

75 FR 78703 - Commission Information Collection Activities, Proposed Collection; Comment Request; Submitted for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

... to Docket No. IC10-542-001. Comments may be filed either electronically or in paper format. Those persons filing electronically do not need to make a paper filing. Documents filed electronically via the... sender's e-mail address upon receipt of comments. For paper filings, the comments should be submitted to...

f-treeGC: a questionnaire-based family tree-creation software for genetic counseling and genome cohort studies.

PubMed

Tokutomi, Tomoharu; Fukushima, Akimune; Yamamoto, Kayono; Bansho, Yasushi; Hachiya, Tsuyoshi; Shimizu, Atsushi

2017-07-14

The Tohoku Medical Megabank project aims to create a next-generation personalized healthcare system by conducting large-scale genome-cohort studies involving three generations of local residents in the areas affected by the Great East Japan Earthquake. We collected medical and genomic information for developing a biobank to be used for this healthcare system. We designed a questionnaire-based pedigree-creation software program named "f-treeGC," which enables even less experienced medical practitioners to accurately and rapidly collect family health history and create pedigree charts. f-treeGC may be run on Adobe AIR. Pedigree charts are created in the following manner: 1) At system startup, the client is prompted to provide required information on the presence or absence of children; f-treeGC is capable of creating a pedigree up to three generations. 2) An interviewer fills out a multiple-choice questionnaire on genealogical information. 3) The information requested includes name, age, gender, general status, infertility status, pregnancy status, fetal status, and physical features or health conditions of individuals over three generations. In addition, information regarding the client and the proband, and birth order information, including multiple gestation, custody, multiple individuals, donor or surrogate, adoption, and consanguinity may be included. 4) f-treeGC shows only marriages between first cousins via the overlay function. 5) f-treeGC automatically creates a pedigree chart, and the chart-creation process is visible for inspection on the screen in real time. 6) The genealogical data may be saved as a file in the original format. The created/modified date and time may be changed as required, and the file may be password-protected and/or saved in read-only format. To enable sorting or searching from the database, the file name automatically contains the terms typed into the entry fields, including physical features or health conditions, by default. 7) Alternatively, family histories are collected using a completed foldable interview paper sheet named "f-sheet", which is identical to the questionnaire in f-treeGC. We developed a questionnaire-based family tree-creation software, named f-treeGC, which is fully compliant with international recommendations for standardized human pedigree nomenclature. The present software simplifies the process of collecting family histories and pedigrees, and has a variety of uses, from genome cohort studies or primary care to genetic counseling.

Data File Standard for Flow Cytometry, version FCS 3.1.

PubMed

Spidlen, Josef; Moore, Wayne; Parks, David; Goldberg, Michael; Bray, Chris; Bierre, Pierre; Gorombey, Peter; Hyun, Bill; Hubbard, Mark; Lange, Simon; Lefebvre, Ray; Leif, Robert; Novo, David; Ostruszka, Leo; Treister, Adam; Wood, James; Murphy, Robert F; Roederer, Mario; Sudar, Damir; Zigon, Robert; Brinkman, Ryan R

2010-01-01

The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. In 1984, the first Flow Cytometry Standard format for data files was adopted as FCS 1.0. This standard was modified in 1990 as FCS 2.0 and again in 1997 as FCS 3.0. We report here on the next generation flow cytometry standard data file format. FCS 3.1 is a minor revision based on suggested improvements from the community. The unchanged goal of the standard is to provide a uniform file format that allows files created by one type of acquisition hardware and software to be analyzed by any other type.The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Changes included in FCS 3.1 address potential ambiguities in the previous versions and provide a more robust standard. The major changes include simplified support for international characters and improved support for storing compensation. The major additions are support for preferred display scale, a standardized way of capturing the sample volume, information about originality of the data file, and support for plate and well identification in high throughput, plate based experiments. Please see the normative version of the FCS 3.1 specification in Supporting Information for this manuscript (or at http://www.isac-net.org/ in the Current standards section) for a complete list of changes.

Data File Standard for Flow Cytometry, Version FCS 3.1

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

Spidlen, Josef; Moore, Wayne; Parks, David

2009-11-10

The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. In 1984, the first Flow Cytometry Standard format for data files was adopted as FCS 1.0. This standard was modified in 1990 as FCS 2.0 and again in 1997 as FCS 3.0. We report here on the next generation flow cytometry standard data file format. FCS 3.1 is a minor revision based on suggested improvements from the community. The unchanged goal of the standard is to provide a uniform file format that allowsmore » files created by one type of acquisition hardware and software to be analyzed by any other type. The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Changes included in FCS 3.1 address potential ambiguities in the previous versions and provide a more robust standard. The major changes include simplified support for international characters and improved support for storing compensation. The major additions are support for preferred display scale, a standardized way of capturing the sample volume, information about originality of the data file, and support for plate and well identification in high throughput, plate based experiments. Please see the normative version of the FCS 3.1 specification in Supporting Information for this manuscript (or at http://www.isac-net.org/ in the Current standards section) for a complete list of changes.« less

GLAD: a system for developing and deploying large-scale bioinformatics grid.

PubMed

Teo, Yong-Meng; Wang, Xianbing; Ng, Yew-Kwong

2005-03-01

Grid computing is used to solve large-scale bioinformatics problems with gigabytes database by distributing the computation across multiple platforms. Until now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. In this study, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), which facilitates the development and deployment of bioinformatics applications on a grid. GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits the task-based parallelism. Two bioinformatics benchmark applications, such as distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.

Particle Pollution

MedlinePlus

... of running) so you don't breathe as hard. Avoid busy roads and highways where PM is usually worse because of emissions from cars and trucks. For more tools to help you learn about air quality, visit Tracking Air Quality . Top of Page File Formats Help: How do I view different file formats ( ...

17 CFR 20.5 - Series S filings.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 17 Commodity and Securities Exchanges 1 2012-04-01 2012-04-01 false Series S filings. 20.5 Section... FOR PHYSICAL COMMODITY SWAPS § 20.5 Series S filings. (a) 102S filing. (1) When a counterparty... 102S filing only once for each counterparty, even if such persons at various times have multiple...

Report of the IAU Commission 4 Working Group on Standardizing Access to Ephemerides and File Format Specification

DTIC Science & Technology

2014-12-01

format for the orientation of a body. It further recommends support- ing data be stored in a text PCK. These formats are used by the SPICE system...INTRODUCTION These file formats were developed for and are used by the SPICE system, developed by the Navigation and Ancillary Information Facility (NAIF...of NASA’s Jet Propulsion Laboratory (JPL). Most users will want to use either the SPICE libraries or CALCEPH, developed by the Institut de mécanique

Personalization of structural PDB files.

PubMed

Woźniak, Tomasz; Adamiak, Ryszard W

2013-01-01

PDB format is most commonly applied by various programs to define three-dimensional structure of biomolecules. However, the programs often use different versions of the format. Thus far, no comprehensive solution for unifying the PDB formats has been developed. Here we present an open-source, Python-based tool called PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one's own PDB versions. PDBinout is freely available under the LGPL licence at http://pdbinout.ibch.poznan.pl.

The Galley Parallel File System

NASA Technical Reports Server (NTRS)

Nieuwejaar, Nils; Kotz, David

1996-01-01

Most current multiprocessor file systems are designed to use multiple disks in parallel, using the high aggregate bandwidth to meet the growing I/0 requirements of parallel scientific applications. Many multiprocessor file systems provide applications with a conventional Unix-like interface, allowing the application to access multiple disks transparently. This interface conceals the parallelism within the file system, increasing the ease of programmability, but making it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. In addition to providing an insufficient interface, most current multiprocessor file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic scientific multiprocessor workloads. We discuss Galley's file structure and application interface, as well as the performance advantages offered by that interface.

14 CFR 221.30 - Passenger fares and charges.

Code of Federal Regulations, 2010 CFR

2010-01-01

... PROCEEDINGS) ECONOMIC REGULATIONS TARIFFS Manner of Filing Tariffs § 221.30 Passenger fares and charges. (a... necessary to carry out the purposes of this part, the applicant carrier to file fare tariffs in a paper format. Such waivers shall only be considered where electronic filing, compared to paper filing, is...

GEWEX-RFA Data File Format and File Naming Convention

Atmospheric Science Data Center

2016-05-20

... documentation, will be stored for each data product. Each time data is added to, removed from, or modified in the file set for a product, ... including 29 days in leap-year Februaries. Time series files containing 15-minute data should start at the top of an hour to ...

TOLNet Data Format for Lidar Ozone Profile & Surface Observations

NASA Astrophysics Data System (ADS)

Chen, G.; Aknan, A. A.; Newchurch, M.; Leblanc, T.

2015-12-01

The Tropospheric Ozone Lidar Network (TOLNet) is an interagency initiative started by NASA, NOAA, and EPA in 2011. TOLNet currently has six Lidars and one ozonesonde station. TOLNet provides high-resolution spatio-temporal measurements of tropospheric (surface to tropopause) ozone and aerosol vertical profiles to address fundamental air-quality science questions. The TOLNet data format was developed by TOLNet members as a community standard for reporting ozone profile observations. The development of this new format was primarily based on the existing NDAAC (Network for the Detection of Atmospheric Composition Change) format and ICARTT (International Consortium for Atmospheric Research on Transport and Transformation) format. The main goal is to present the Lidar observations in self-describing and easy-to-use data files. The TOLNet format is an ASCII format containing a general file header, individual profile headers, and the profile data. The last two components repeat for all profiles recorded in the file. The TOLNet format is both human and machine readable as it adopts standard metadata entries and fixed variable names. In addition, software has been developed to check for format compliance. To be presented is a detailed description of the TOLNet format protocol and scanning software.

47 CFR 14.52 - Copies; service; separate filings against multiple defendants.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false Copies; service; separate filings against multiple defendants. 14.52 Section 14.52 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Recordkeeping, Consumer...

47 CFR 14.52 - Copies; service; separate filings against multiple defendants.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 1 2012-10-01 2012-10-01 false Copies; service; separate filings against multiple defendants. 14.52 Section 14.52 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Recordkeeping, Consumer...

47 CFR 14.52 - Copies; service; separate filings against multiple defendants.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 1 2013-10-01 2013-10-01 false Copies; service; separate filings against multiple defendants. 14.52 Section 14.52 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Recordkeeping, Consumer...

j5 v2.8.4

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

Hillson, Nathan

j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding),more » designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputs a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.« less

46 CFR 535.701 - General requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., Washington, DC 20573-0001. A copy of the Monitoring Report form in Microsoft Word and Excel format may be... Monitoring Reports in the Commission's prescribed electronic format, either on diskette or CD-ROM. (e)(1) The... filed by this subpart may be filed by direct electronic transmission in lieu of hard copy. Detailed...

Standard Electronic Format Specification for Tank Characterization Data Loader Version 3.5

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

ADAMS, M.R.

2001-01-31

The purpose of this document is to describe the standard electronic format for data files that will be sent for entry into the Tank Characterization Database (TCD). There are 2 different file types needed for each data load: (1) Analytical Results and (2) Sample Descriptions.

47 CFR 1.913 - Application and notification forms; electronic and manual filing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... notifications whenever possible. The files, other than the ASCII table of contents, should be in Adobe Acrobat... possible. The attachment should be uploaded via ULS in Adobe Acrobat Portable Document Format (PDF... the table of contents, should be in Adobe Acrobat Portable Document Format (PDF) whenever possible...

9 CFR 124.30 - Filing, format, and content of petitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... RESTORATION Due Diligence Petitions § 124.30 Filing, format, and content of petitions. (a) Any interested... diligence in seeking APHIS approval of the product during the regulatory review period. (b) The petition... subpart. (c) The petition must allege that the applicant failed to act with due diligence sometime during...

Viewing Files — EDRN Public Portal

Cancer.gov

In addition to standard HTML Web pages, our web site contain other file formats. You may need additional software or browser plug-ins to view some of the information available on our site. This document lists show each format, along with links to the corresponding freely available plug-ins or viewers.

Painless File Extraction: The A(rc)--Z(oo) of Internet Archive Formats.

ERIC Educational Resources Information Center

Simmonds, Curtis

1993-01-01

Discusses extraction programs needed to postprocess software downloaded from the Internet that has been archived and compressed for the purposes of storage and file transfer. Archiving formats for DOS, Macintosh, and UNIX operating systems are described; and cross-platform compression utilities are explained. (LRW)

SiLK: A Tool Suite for Unsampled Network Flow Analysis at Scale

DTIC Science & Technology

2014-06-01

file format,” [Accessed: Feb 9, 2014]. [Online]. Available: https: //tools.netsa.cert.org/silk/faq.html#file-formats [12] “2012 data breach investigations...report (DBIR),” Verizon, Tech. Rep., 2012. [Online]. Available: http://www.verizonenterprise.com/DBIR/2012/ [13] “2013 data breach investigations

Incidence of apical crack formation and propagation during removal of root canal filling materials with different engine driven nickel-titanium instruments.

PubMed

Özyürek, Taha; Tek, Vildan; Yılmaz, Koray; Uslu, Gülşah

2017-11-01

To determine the incidence of crack formation and propagation in apical root dentin after retreatment procedures performed using ProTaper Universal Retreatment (PTR), Mtwo-R, ProTaper Next (PTN), and Twisted File Adaptive (TFA) systems. The study consisted of 120 extracted mandibular premolars. One millimeter from the apex of each tooth was ground perpendicular to the long axis of the tooth, and the apical surface was polished. Twenty teeth served as the negative control group. One hundred teeth were prepared, obturated, and then divided into 5 retreatment groups. The retreatment procedures were performed using the following files: PTR, Mtwo-R, PTN, TFA, and hand files. After filling material removal, apical enlargement was done using apical size 0.50 mm ProTaper Universal (PTU), Mtwo, PTN, TFA, and hand files. Digital images of the apical root surfaces were recorded before preparation, after preparation, after obturation, after filling removal, and after apical enlargement using a stereomicroscope. The images were then inspected for the presence of new apical cracks and crack propagation. Data were analyzed with χ 2 tests using SPSS 21.0 software. New cracks and crack propagation occurred in all the experimental groups during the retreatment process. Nickel-titanium rotary file systems caused significantly more apical crack formation and propagation than the hand files. The PTU system caused significantly more apical cracks than the other groups after the apical enlargement stage. This study showed that retreatment procedures and apical enlargement after the use of retreatment files can cause crack formation and propagation in apical dentin.

Enhanced Modeling of First-Order Plant Equations of Motion for Aeroelastic and Aeroservoelastic Applications

NASA Technical Reports Server (NTRS)

Pototzky, Anthony S.

2010-01-01

A methodology is described for generating first-order plant equations of motion for aeroelastic and aeroservoelastic applications. The description begins with the process of generating data files representing specialized mode-shapes, such as rigid-body and control surface modes, using both PATRAN and NASTRAN analysis. NASTRAN executes the 146 solution sequence using numerous Direct Matrix Abstraction Program (DMAP) calls to import the mode-shape files and to perform the aeroelastic response analysis. The aeroelastic response analysis calculates and extracts structural frequencies, generalized masses, frequency-dependent generalized aerodynamic force (GAF) coefficients, sensor deflections and load coefficients data as text-formatted data files. The data files are then re-sequenced and re-formatted using a custom written FORTRAN program. The text-formatted data files are stored and coefficients for s-plane equations are fitted to the frequency-dependent GAF coefficients using two Interactions of Structures, Aerodynamics and Controls (ISAC) programs. With tabular files from stored data created by ISAC, MATLAB generates the first-order aeroservoelastic plant equations of motion. These equations include control-surface actuator, turbulence, sensor and load modeling. Altitude varying root-locus plot and PSD plot results for a model of the F-18 aircraft are presented to demonstrate the capability.

Extract and visualize geolocation from any text file

NASA Astrophysics Data System (ADS)

Boustani, M.

2015-12-01

There are variety of text file formats such as PDF, HTML and more which contains words about locations(countries, cities, regions and more). GeoParser developed as one of sub-projects under DARPA Memex to help finding any geolocation information crawled website data. It is a web application benefiting from Apache Tika to extract locations from any text file format and visualize geolocations on the map. https://github.com/MBoustani/GeoParserhttps://github.com/chrismattmann/tika-pythonhttp://www.darpa.mil/program/memex

MT3DMS: A Modular Three-Dimensional Multispecies Transport Model for Simulation of Advection, Dispersion, and Chemical Reactions of Contaminants in Groundwater Systems; Documentation and User’s Guide

DTIC Science & Technology

1999-12-01

addition, the data files saved in the POINT format can include an optional header which is compatible with Amtec Engineering’s 2-D and 3-D visualization...34.DAT" file so that the file can be used directly by Amtec Engineering’s 2-D and 3-D visualization package Tecplot©. The ARRAY and POINT formats are

Can ASCII data files be standardized for Earth Science?

NASA Astrophysics Data System (ADS)

Evans, K. D.; Chen, G.; Wilson, A.; Law, E.; Olding, S. W.; Krotkov, N. A.; Conover, H.

2015-12-01

NASA's Earth Science Data Systems Working Groups (ESDSWG) was created over 10 years ago. The role of the ESDSWG is to make recommendations relevant to NASA's Earth science data systems from user experiences. Each group works independently focusing on a unique topic. Participation in ESDSWG groups comes from a variety of NASA-funded science and technology projects, such as MEaSUREs, NASA information technology experts, affiliated contractor, staff and other interested community members from academia and industry. Recommendations from the ESDSWG groups will enhance NASA's efforts to develop long term data products. Each year, the ESDSWG has a face-to-face meeting to discuss recommendations and future efforts. Last year's (2014) ASCII for Science Data Working Group (ASCII WG) completed its goals and made recommendations on a minimum set of information that is needed to make ASCII files at least human readable and usable for the foreseeable future. The 2014 ASCII WG created a table of ASCII files and their components as a means for understanding what kind of ASCII formats exist and what components they have in common. Using this table and adding information from other ASCII file formats, we will discuss the advantages and disadvantages of a standardized format. For instance, Space Geodesy scientists have been using the same RINEX/SINEX ASCII format for decades. Astronomers mostly archive their data in the FITS format. Yet Earth scientists seem to have a slew of ASCII formats, such as ICARTT, netCDF (an ASCII dump) and the IceBridge ASCII format. The 2015 Working Group is focusing on promoting extendibility and machine readability of ASCII data. Questions have been posed, including, Can we have a standardized ASCII file format? Can it be machine-readable and simultaneously human-readable? We will present a summary of the current used ASCII formats in terms of advantages and shortcomings, as well as potential improvements.

As-built design specification for PARCLS

NASA Technical Reports Server (NTRS)

Tompkins, M. A. (Principal Investigator)

1981-01-01

The PARCLS program, part of the CLASFYG package, reads a parameter file created by the CLASFYG program and a pure pixel ground truth file in order to create to classification file of three separate crop categories in universal format.

27 CFR 46.235 - Filing requirements for multiple locations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... TOBACCO PRODUCTS AND CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette Tubes Held for Sale on April 1, 2009 Filing Requirements § 46.235 Filing...

27 CFR 46.235 - Filing requirements for multiple locations.

Code of Federal Regulations, 2012 CFR

2012-04-01

... TOBACCO PRODUCTS AND CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette Tubes Held for Sale on April 1, 2009 Filing Requirements § 46.235 Filing...

27 CFR 46.235 - Filing requirements for multiple locations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... TOBACCO PRODUCTS AND CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette Tubes Held for Sale on April 1, 2009 Filing Requirements § 46.235 Filing...

27 CFR 46.235 - Filing requirements for multiple locations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... TOBACCO PRODUCTS AND CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette Tubes Held for Sale on April 1, 2009 Filing Requirements § 46.235 Filing...

27 CFR 46.235 - Filing requirements for multiple locations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... TOBACCO PRODUCTS AND CIGARETTE PAPERS AND TUBES Floor Stocks Tax on Certain Tobacco Products, Cigarette Papers, and Cigarette Tubes Held for Sale on April 1, 2009 Filing Requirements § 46.235 Filing...

Analytic Patch Configuration (APC) gateway version 1.0 user's guide

NASA Technical Reports Server (NTRS)

Bingel, Bradford D.

1990-01-01

The Analytic Patch Configuration (APC) is an interactive software tool which translates aircraft configuration geometry files from one format into another. This initial release of the APC Gateway accommodates six formats: the four accepted APC formats (89f, 89fd, 89u, and 89ud), the PATRAN 2.x phase 1 neutral file format, and the Integrated Aerodynamic Analysis System (IAAS) General Geometry (GG) format. Written in ANSI FORTRAN 77 and completely self-contained, the APC Gateway is very portable and was already installed on CDC/NOS, VAX/VMS, SUN, SGI/IRIS, CONVEX, and GRAY hosts.

Integration of DICOM and openEHR standards

NASA Astrophysics Data System (ADS)

Wang, Ying; Yao, Zhihong; Liu, Lei

2011-03-01

The standard format for medical imaging storage and transmission is DICOM. openEHR is an open standard specification in health informatics that describes the management and storage, retrieval and exchange of health data in electronic health records. Considering that the integration of DICOM and openEHR is beneficial to information sharing, on the basis of XML-based DICOM format, we developed a method of creating a DICOM Imaging Archetype in openEHR to enable the integration of DICOM and openEHR. Each DICOM file contains abundant imaging information. However, because reading a DICOM involves looking up the DICOM Data Dictionary, the readability of a DICOM file has been limited. openEHR has innovatively adopted two level modeling method, making clinical information divided into lower level, the information model, and upper level, archetypes and templates. But one critical challenge posed to the development of openEHR is the information sharing problem, especially in imaging information sharing. For example, some important imaging information cannot be displayed in an openEHR file. In this paper, to enhance the readability of a DICOM file and semantic interoperability of an openEHR file, we developed a method of mapping a DICOM file to an openEHR file by adopting the form of archetype defined in openEHR. Because an archetype has a tree structure, after mapping a DICOM file to an openEHR file, the converted information is structuralized in conformance with openEHR format. This method enables the integration of DICOM and openEHR and data exchange without losing imaging information between two standards.

78 FR 13933 - Railroad Cost of Capital-2012

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-01

... by May 31, 2013. ADDRESSES: Comments may be submitted either via the Board's e-filing system or in the traditional paper format. Any person using e-filing should comply with the instructions at the E-FILING link on the Board's Web site, at http://www.stb.dot.gov . Any person submitting a filing in the...

76 FR 10430 - Railroad Cost of Capital-2010

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-24

... by June 8, 2011. ADDRESSES: Comments may be submitted either via the Board's e-filing system or in the traditional paper format. Any person using e-filing should comply with the instructions at the E-FILING link on the Board's Web site, at http://www.stb.dot.gov . Any person submitting a filing in the...

75 FR 16894 - Railroad Cost of Capital-2009

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-02

... 15, 2010. ADDRESSES: Comments may be submitted either via the Board's e-filing system or in the traditional paper format. Any person using e-filing should comply with the instructions at the E-FILING link on the Board's Web site, at http://www.stb.dot.gov . Any person submitting a filing in the...

5 CFR 1201.14 - Electronic filing procedures.

Code of Federal Regulations, 2014 CFR

2014-01-01

...-Appeal Online, in which case service is governed by paragraph (j) of this section, or by non-electronic... (PDF), and image files (files created by scanning). A list of formats allowed can be found at e-Appeal... representatives of the appeals in which they were filed. (j) Service of electronic pleadings and MSPB documents...

5 CFR 1201.14 - Electronic filing procedures.

Code of Federal Regulations, 2013 CFR

2013-01-01

...-Appeal Online, in which case service is governed by paragraph (j) of this section, or by non-electronic... (PDF), and image files (files created by scanning). A list of formats allowed can be found at e-Appeal... representatives of the appeals in which they were filed. (j) Service of electronic pleadings and MSPB documents...

5 CFR 1201.14 - Electronic filing procedures.

Code of Federal Regulations, 2011 CFR

2011-01-01

...-Appeal Online, in which case service is governed by paragraph (j) of this section, or by non-electronic... (PDF), and image files (files created by scanning). A list of formats allowed can be found at e-Appeal... representatives of the appeals in which they were filed. (j) Service of electronic pleadings and MSPB documents...

5 CFR 1201.14 - Electronic filing procedures.

Code of Federal Regulations, 2012 CFR

2012-01-01

...-Appeal Online, in which case service is governed by paragraph (j) of this section, or by non-electronic... (PDF), and image files (files created by scanning). A list of formats allowed can be found at e-Appeal... representatives of the appeals in which they were filed. (j) Service of electronic pleadings and MSPB documents...

Converting Inhouse Subject Card Files to Electronic Keyword Files.

ERIC Educational Resources Information Center

Culmer, Carita M.

The library at Phoenix College developed the Controversial Issues Files (CIF), a "home made" card file containing references pertinent to specific ongoing assignments. Although the CIF had proven itself to be an excellent resource tool for beginning researchers, it was cumbersome to maintain in the card format, and was limited to very…

Networks for Autonomous Formation Flying Satellite Systems

NASA Technical Reports Server (NTRS)

Knoblock, Eric J.; Konangi, Vijay K.; Wallett, Thomas M.; Bhasin, Kul B.

2001-01-01

The performance of three communications networks to support autonomous multi-spacecraft formation flying systems is presented. All systems are comprised of a ten-satellite formation arranged in a star topology, with one of the satellites designated as the central or "mother ship." All data is routed through the mother ship to the terrestrial network. The first system uses a TCP/lP over ATM protocol architecture within the formation the second system uses the IEEE 802.11 protocol architecture within the formation and the last system uses both of the previous architectures with a constellation of geosynchronous satellites serving as an intermediate point-of-contact between the formation and the terrestrial network. The simulations consist of file transfers using either the File Transfer Protocol (FTP) or the Simple Automatic File Exchange (SAFE) Protocol. The results compare the IF queuing delay, and IP processing delay at the mother ship as well as application-level round-trip time for both systems, In all cases, using IEEE 802.11 within the formation yields less delay. Also, the throughput exhibited by SAFE is better than FTP.

Central Satellite Data Repository Supporting Research and Development

NASA Astrophysics Data System (ADS)

Han, W.; Brust, J.

2015-12-01

Near real-time satellite data is critical to many research and development activities of atmosphere, land, and ocean processes. Acquiring and managing huge volumes of satellite data without (or with less) latency in an organization is always a challenge in the big data age. An organization level data repository is a practical solution to meeting this challenge. The STAR (Center for Satellite Applications and Research of NOAA) Central Data Repository (SCDR) is a scalable, stable, and reliable repository to acquire, manipulate, and disseminate various types of satellite data in an effective and efficient manner. SCDR collects more than 200 data products, which are commonly used by multiple groups in STAR, from NOAA, GOES, Metop, Suomi NPP, Sentinel, Himawari, and other satellites. The processes of acquisition, recording, retrieval, organization, and dissemination are performed in parallel. Multiple data access interfaces, like FTP, FTPS, HTTP, HTTPS, and RESTful, are supported in the SCDR to obtain satellite data from their providers through high speed internet. The original satellite data in various raster formats can be parsed in the respective adapter to retrieve data information. The data information is ingested to the corresponding partitioned tables in the central database. All files are distributed equally on the Network File System (NFS) disks to balance the disk load. SCDR provides consistent interfaces (including Perl utility, portal, and RESTful Web service) to locate files of interest easily and quickly and access them directly by over 200 compute servers via NFS. SCDR greatly improves collection and integration of near real-time satellite data, addresses satellite data requirements of scientists and researchers, and facilitates their primary research and development activities.

A Digital Control Algorithm for Magnetic Suspension Systems

NASA Technical Reports Server (NTRS)

Britton, Thomas C.

1996-01-01

An ongoing program exists to investigate and develop magnetic suspension technologies and modelling techniques at NASA Langley Research Center. Presently, there is a laboratory-scale large air-gap suspension system capable of five degree-of-freedom (DOF) control that is operational and a six DOF system that is under development. Those systems levitate a cylindrical element containing a permanent magnet core above a planar array of electromagnets, which are used for levitation and control purposes. In order to evaluate various control approaches with those systems, the Generic Real-Time State-Space Controller (GRTSSC) software package was developed. That control software package allows the user to implement multiple control methods and allows for varied input/output commands. The development of the control algorithm is presented. The desired functionality of the software is discussed, including the ability to inject noise on sensor inputs and/or actuator outputs. Various limitations, common issues, and trade-offs are discussed including data format precision; the drawbacks of using either Direct Memory Access (DMA), interrupts, or program control techniques for data acquisition; and platform dependent concerns related to the portability of the software, such as memory addressing formats. Efforts to minimize overall controller loop-rate and a comparison of achievable controller sample rates are discussed. The implementation of a modular code structure is presented. The format for the controller input data file and the noise information file is presented. Controller input vector information is available for post-processing by mathematical analysis software such as MATLAB1.

Common Filing Deficiencies in Abbreviated New Drug Applications Containing Clinical Endpoint Studies.

PubMed

Fermaglich, Lewis J; Chen, Ru; Kim, Carol Y; Chuh, Eunjung Esther; Thomas, Teena; Shetty, Daiva; Lee, Julia; Young, Johnny; Fan, Ying

2018-01-01

The objective of this report is to summarize common deficiencies identified in the filing reviews of abbreviated new drug applications (ANDAs) with clinical endpoint bioequivalence studies and skin irritation, sensitization, and adhesion (I/S/A) studies received by the US Food and Drug Administration (FDA) between 2007 and 2017, to help applicants avoid common deficiencies, minimize "refuse-to-receive" (RTR) actions, "information requests," and ANDA approval delays. Multiple internal FDA databases were searched to evaluate and summarize common deficiencies identified in ANDA submissions containing clinical endpoint studies and skin I/S/A studies that required review by the Division of Clinical Review. A total of 275 ANDA submissions with filing reviews from January 2007 to June 2017 were analyzed in this report. Two hundred eighteen (79.3%) filing reviews contained one or more deficiencies. Seventy-nine (28.7%) ANDAs were issued RTR letters because of major clinical deficiencies, specifically bioequivalence and clinical deficiencies, accounting for 9% of overall identified deficiencies. Twenty-two other categories of deficiencies are summarized into 4 main categories: missing information related to the clinical studies other than data sets (38%), missing data sets (35%), formulation issues (12%), and organization/format issues (6%). The most common deficiency in the "missing information related to the clinical studies other than data sets" category was "missing clarification of information" (22%). We also noted that the Division of Filing Review has identified these same types of deficiencies since assuming responsibility of the filing assessment for ANDAs with clinical endpoint BE studies and skin I/S/A studies. In conclusion, to minimize "refuse-to-receive" actions, "information requests," and approval of ANDA delays for generic drug products, applicants should submit full clinical study reports, including all data sets for drug products recommending clinical studies.

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files.

PubMed

Sun, Xiaobo; Gao, Jingjing; Jin, Peng; Eng, Celeste; Burchard, Esteban G; Beaty, Terri H; Ruczinski, Ingo; Mathias, Rasika A; Barnes, Kathleen; Wang, Fusheng; Qin, Zhaohui S

2018-06-01

Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of variant call format (VCF) files is frequently required in large-scale whole-genome sequencing or whole-exome sequencing projects. Traditional single-machine based methods become increasingly inefficient when processing large numbers of files due to the excessive computation time and Input/Output bottleneck. Distributed systems and more recent cloud-based systems offer an attractive solution. However, carefully designed and optimized workflow patterns and execution plans (schemas) are required to take full advantage of the increased computing power while overcoming bottlenecks to achieve high performance. In this study, we custom-design optimized schemas for three Apache big data platforms, Hadoop (MapReduce), HBase, and Spark, to perform sorted merging of a large number of VCF files. These schemas all adopt the divide-and-conquer strategy to split the merging job into sequential phases/stages consisting of subtasks that are conquered in an ordered, parallel, and bottleneck-free way. In two illustrating examples, we test the performance of our schemas on merging multiple VCF files into either a single TPED or a single VCF file, which are benchmarked with the traditional single/parallel multiway-merge methods, message passing interface (MPI)-based high-performance computing (HPC) implementation, and the popular VCFTools. Our experiments suggest all three schemas either deliver a significant improvement in efficiency or render much better strong and weak scalabilities over traditional methods. Our findings provide generalized scalable schemas for performing sorted merging on genetics and genomics data using these Apache distributed systems.

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files

PubMed Central

Gao, Jingjing; Jin, Peng; Eng, Celeste; Burchard, Esteban G; Beaty, Terri H; Ruczinski, Ingo; Mathias, Rasika A; Barnes, Kathleen; Wang, Fusheng

2018-01-01

Abstract Background Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of variant call format (VCF) files is frequently required in large-scale whole-genome sequencing or whole-exome sequencing projects. Traditional single-machine based methods become increasingly inefficient when processing large numbers of files due to the excessive computation time and Input/Output bottleneck. Distributed systems and more recent cloud-based systems offer an attractive solution. However, carefully designed and optimized workflow patterns and execution plans (schemas) are required to take full advantage of the increased computing power while overcoming bottlenecks to achieve high performance. Findings In this study, we custom-design optimized schemas for three Apache big data platforms, Hadoop (MapReduce), HBase, and Spark, to perform sorted merging of a large number of VCF files. These schemas all adopt the divide-and-conquer strategy to split the merging job into sequential phases/stages consisting of subtasks that are conquered in an ordered, parallel, and bottleneck-free way. In two illustrating examples, we test the performance of our schemas on merging multiple VCF files into either a single TPED or a single VCF file, which are benchmarked with the traditional single/parallel multiway-merge methods, message passing interface (MPI)–based high-performance computing (HPC) implementation, and the popular VCFTools. Conclusions Our experiments suggest all three schemas either deliver a significant improvement in efficiency or render much better strong and weak scalabilities over traditional methods. Our findings provide generalized scalable schemas for performing sorted merging on genetics and genomics data using these Apache distributed systems. PMID:29762754

37 CFR 1.615 - Format of papers filed in a supplemental examination proceeding.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Format of papers filed in a supplemental examination proceeding. 1.615 Section 1.615 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES...

75 FR 14386 - Interpretation of Transmission Planning Reliability Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-25

... created electronically using word processing software should be filed in native applications or print-to.... FERC, 564 F.3d 1342 (DC Cir. 2009). \\6\\ Mandatory Reliability Standards for the Bulk-Power System... print-to-PDF format and not in a scanned format. Commenters filing electronically do not need to make a...

PROPOSED STANDARD TO GREATLY EXPAND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT

EPA Science Inventory

PROPOSED ST ANDARD TO GREA TL Y EXP AND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT

The ability to assess the potential toxicity of environmental, pharmaceutical, or industrial chemicals based on chemical structure in...

37 CFR 1.615 - Format of papers filed in a supplemental examination proceeding.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Format of papers filed in a supplemental examination proceeding. 1.615 Section 1.615 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES...

VizieR Online Data Catalog: Metal enrichment in semi-analytical model (Cousin+, 2016)

NASA Astrophysics Data System (ADS)

Cousin, M.; Buat, V.; Boissier, S.; Bethermin, M.; Roehlly, Y. Genois M.

2016-04-01

The repository contains outputs from the different models: - m1: Classical (only hot gas) isotropic accretion scenario + Standard Shmidt Kennicutt law - m2: Bimodal accretion (cold streams) + Standard Shmidt Kennicutt law - m3: Classical (only hot gas) isotropic accretion scenario + ad-hoc non-star forming gas reservoir - m4: Bimodal accretion (cold streams) + ad-hoc non-star forming gas reservoir For each model of these models dada are saved in eGalICS_m*.fits file. All these fits-formated files are compatible with the TOPCAT software available on: http://www.star.bris.ac.uk/~mbt/topcat/ We also provide, for each Initial Mass Function available, a set of two fits-formated files associated to the chemodynamical library presented in the paper. For these two files, data are available for all metallicity bins used. - masslossrates_IMF.fits: The instantaneous total ejecta rate associated to a SSP for the six different main-ISM elements. - SNratesIMF.fits: The total SN rate (SNII+SNIa [nb/Gyr]) associated to a SSP, individual contribution of SNII and SNIa are also given. These files are available for four different IMFs: Salpeter+55 (1955ApJ...121..161S), Chabrier+03 (2003PASP..115..763C), Kroupa+93 (2001MNRAS.322..231K) and Scalo+98 (1998ASPC..142..201S. Both ejecta rates and SN rates are computed for the complete list of stellar ages provided in the BC03 spectra library. They are saved in fits-formated files and structured with different extensions corresponding to the different initial stellar metallicity bins. We finally provide the median star formation history, the median gas accretion history and the metal enrichment histories associated to our MW-sisters sample: MWsistershistories.dat If you used data associated to eGalICS semi-analytic model, please cite the following paper: Cousin et al., 2015A&A...575A..33C, "Toward a new modelling of gas flows in a semi-analytical model of galaxy formation and evolution" (3 data files).

IVS Working Group 4: VLBI Data Structures

NASA Astrophysics Data System (ADS)

Gipson, J.

2012-12-01

I present an overview of the "openDB format" for storing, archiving, and processing VLBI data. In this scheme, most VLBI data is stored in NetCDF files. NetCDF has the advantage that there are interfaces to most common computer languages including Fortran, Fortran-90, C, C++, Perl, etc, and the most common operating systems including Linux, Windows, and Mac. The data files for a particular session are organized by special ASCII "wrapper" files which contain pointers to the data files. This allows great flexibility in the processing and analysis of VLBI data. For example it allows you to easily change subsets of the data used in the analysis such as troposphere modeling, ionospheric calibration, editing, and ambiguity resolution. It also allows for extending the types of data used, e.g., source maps. I present a roadmap to transition to this new format. The new format can already be used by VieVS and by the global mode of solve. There are plans in work for other software packages to be able to use the new format.

CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

PubMed

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

2011-05-01

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

Segy-change: The swiss army knife for the SEG-Y files

NASA Astrophysics Data System (ADS)

Stanghellini, Giuseppe; Carrara, Gabriela

Data collected during active and passive seismic surveys can be stored in many different, more or less standard, formats. One of the most popular is the SEG-Y format, developed since 1975 to store single-line seismic digital data on tapes, and now evolved to store them into hard-disk and other media as well. Unfortunately, sometimes, files that are claimed to be recorded in the SEG-Y format cannot be processed using available free or industrial packages. Aiming to solve this impasse we present segy-change, a pre-processing software program to view, analyze, change and fix errors present in SEG-Y data files. It is written in C language and it can be used also as a software library and is compatible with most operating systems. Segy-change allows the user to display and optionally change the values inside all parts of a SEG-Y file: the file header, the trace headers and the data blocks. In addition, it allows to do a quality check on the data by plotting the traces. We provide instructions and examples on how to use the software.

VizieR Online Data Catalog: Opacities from the Opacity Project (Seaton+, 1995)

NASA Astrophysics Data System (ADS)

Seaton, M. J.; Yan, Y.; Mihalas, D.; Pradhan, A. K.

1997-08-01

1 CODES. ***** 1.1 Code rop.for ************ This code reads opacity files written in standard OP format. Its main purpose is to provide documentation on the contents of the files. This code, like the other codes provided, prompts for the name of the file (or files) to be read. The file names read in response to the prompt may have up to 128 characters. 1.2 Code opfit.for ************** This code reads opacity files in standard OP format, and provides for interpolation of opacities to any required values of temperature and mass-density. The method used is described in OPF. The code prompts for the name of a file giving all required control parameters. As an example, the file opfit.dat is provided (users will need to change directory names and file names). The use of opfit.for is illustrated using opfit.dat. Most users will probably want to adapt opfit.for for use as a subroutine in other codes. Timings for DEC 7000 ALPHA: 0.3 sec for data read and initialisations; then 0.0007 sec for each temperature-density point. Users who like OPAL formats should note that opfit.for has a facility to produce files of OP data in OPAL-type formats. 1.3 Code ixz.for ************ This code provides for interpolations to any required values of X and Z. See IXZ. It prompts for the name of a file giving all required control parameters. An example of such a file if provided, ixz.dat (the user will need to change directory and file names). The output files have names s92INT.'nnn'. The user specifies the first value of nnn, and the number of files to be produced. 2. DATA FILES ********** 2.1 Data files for solar metal-mix ****************************** Data for solar metal-mix s92 as defined in SYMP. These files are from version 2 runs of December 1994 (see IXZ for details on Version 2). There are 213 files with names s92.'nnn', 'nnn'=201 to 413. Each file occupies 83762 bytes. The file s92.version2 gives values of X (hydrogen mass-faction) and Z (metals mass-fraction) for each value of 'nnn'. The user can get s92.version2, select the values of 'nnn' required, then get the required files s92.'nnn'. The user can see the file in ftp, displayed on the screen, by typing "get s92.version2 -". The files s92.'nnn' can be used with opfit.for to obtain opacities for any requires value of temperature and mass density. Files for other metal-mixtures will be added in due course. Send requests to mjs@star.ucl.ac.uk. 2.2 Files for interpolation in X and Z ********************************** The data files have names s92xz.'mmm', where 'mmm'=001 to 096. They differ from the standard OP files (such as s92.'nnn' --- section 2.1 above) in that they contain information giving derivatives of opacities with respect to X and Z. Each file s92xz.'mmm' occupies 148241 bytes. The interpolations to any required values of X and Z are made using ixz.for. Timings: on DEC 7000 ALPHA, 2.16 sec for each new-mixture file. For interpolations to some specified values of X and Z, one requires just 4 files s92xz.'mmm'. Most users will not require the complete set of files s92xz.'mmm'. The file s92xz.index includes a table (starting on line 3) giving values, for each 'mmm' file, of x,y,z (abundances by number-factions) and X,Y,Z (abundances by mass-fractions). Users are advised to get the file s92.index, and select values of 'mmm' for files required, then get those files. The files produced by ixz.for are in standard OP format and can be used with opfit.for to obtain opacities for any required values of temperature and mass density. 3 RECOMMENDED PROCEDURE FOR USE OF OPACITY FILES ********************************************** (1) Get the file s92.version2. (2) If the values of X and Z you require are available in the files s92.'nnn' then get those files. (3) If not, get the file s92xz.index. (4) Select from s92xz.index the values of 'mmm' which cover the range of X and Z in which your are interested. Get those files and use ixz.for to generate files for your exact required values of X and Z. (5) Note that the exact abundance mixtures used are specified in each file (see rop.for). Also each run of opfit.for produces a table of abundances. (6) If you want a metal-mix different from that of s92, contact mjs@star.ucl.ac.uk. 4 FUTURE DEVELOPMENTS ******************* (1) Data for the calculation of radiative forces are provided as the CDS catalog (added August 1997) (2) Facilities will be added later which will enable the user to make calculations giving files for any required mixtures. (9 data files).

Web Standard: PDF - When to Use, Document Metadata, PDF Sections

EPA Pesticide Factsheets

PDF files provide some benefits when used appropriately. PDF files should not be used for short documents ( 5 pages) unless retaining the format for printing is important. PDFs should have internal file metadata and meet section 508 standards.

Anisoft - Advanced Treatment of Magnetic Anisotropy Data

NASA Astrophysics Data System (ADS)

Chadima, M.

2017-12-01

Since its first release, Anisoft (Anisotropy Data Browser) has gained a wide popularity in magnetic fabric community mainly due to its simple and user-friendly interface enabling very fast visualization of magnetic anisotropy tensors. Here, a major Anisoft update is presented transforming a rather simple data viewer into a platform offering an advanced treatment of magnetic anisotropy data. The updated software introduces new enlarged binary data format which stores both in-phase and out-of-phase (if measured) susceptibility tensors (AMS) or tensors of anisotropy of magnetic remanence (AMR) together with their respective confidence ellipses and values of F-tests for anisotropy. In addition to the tensor data, a whole array of specimen orientation angles, orientation of mesoscopic foliation(s) and lineation(s) is stored for each record enabling later editing or corrections. The input data may be directly acquired by AGICO Kappabridges (AMS) or Spinner Magnetometers (AMR); imported from various data formats, including the long-time standard binary ran-format; or manually created. Multiple anisotropy files can be combined together or split into several files by manual data selection or data filtering according to their values. Anisotropy tensors are conventionally visualized as principal directions (eigenvectors) in equal-area projection (stereoplot) together with a wide array of quantitative anisotropy parameters presented in histograms or in color-coded scatter plots showing mutual relationship of up to three quantitative parameters. When dealing with AMS in variable low fields, field-independent and field-dependent components of anisotropy can be determined (Hrouda 2009). For a group of specimens, individual principal directions can be contoured, or a mean tensor and respective confidence ellipses of its principal directions can be calculated using either the Hext-Jelinek (Jelinek 1978) statistics or the Bootstrap method (Constable & Tauxe 1990). Each graphical output can be exported into several vector or raster graphical formats or, via clipboard, pasted directly into a presentation or publication manuscript. Calculated principal directions or anisotropy parameters can be exported into various types of text files ready to be visualized or processed by any software of user's choice.

Guide to GFS History File Change on May 1, 2007

Science.gov Websites

Guide to GFS History File Change on May 1, 2007 On May 1, 2007 12Z, the GFS had a major change. The change caused the internal binary GFS history file to change formats. The file is still in spectral space but now pressure is calculated in a different way. Sometime in the future, the GFS history file may be

FGGE/ERBZ tape specification and shipping letter description

NASA Technical Reports Server (NTRS)

Han, D.; Lo, H.

1983-01-01

The FGGE/ERBZ tape contains 5 parameters which are extracted and reformatted from the Nimbus-7 ERB Zonal Means Tape. There are three types of files on a FGGE/ERBZ tape: a tape header file, and data files. Physical characteristics, gross format, and file specifications are given. A sample tape check/document printout (shipping letter) is included.

NCEP BUFR File Structure

Science.gov Websites

. These tables may be defined within a separate ASCII text file (see Description and Format of BUFR Tables time, the BUFR tables are usually read from an external ASCII text file (although it is also possible reports. Click here to view the ASCII text file (called /nwprod/fix/bufrtab.002 on the NCEP CCS machines

75 FR 45609 - Commission Information Collection Activities (FERC-542); Comment Request; Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-03

... electronically (eFiled) or in paper format, and should refer to Docket No. IC10-542-000. Documents must be.... Commenters making an eFiling should not make a paper filing. Commenters that are not able to file electronically must send an original and two (2) paper copies of their comments to: Federal Energy Regulatory...

Global Paleoclimatic Data for 6000 Yr B.P. (1985) (NDP-011)

DOE Data Explorer

Webb, III, T. [Department of Geological Sciences, Brown University, Providence, Rhode Island (USA)

2012-01-01

To determine regional and global climatic variations during the past 6000 years, pollen, lake level, and marine plankton data from 797 stations were compiled to form a global data set. Radiocarbon dating and dated tephras were used to determine the ages of the specimens. The data available for the pollen data are site number, site name, latitude, longitude, elevation, and percentages of various taxa. For lake-level data, the data are site number, site name, latitude, longitude, and lake-level status. And for marine plankton, the data are site number, site name, latitude, longitude, water depth, date, dating control code, depth of sample, interpolated age of sample, estimated winter and summer sea-surface temperatures, and percentages of various taxa. The data are in 55 files: 5 files for each of 9 geographic regions and 10 supplemental files. The files for each region include (1) a FORMAT file describing the format and contents of the data for that region, (2) an INDEX file containing descriptive information about each site and its data, (3) a DATA file containing the data and available climatic estimates, (4) a PUBINDEX file indexing the bibliographic references associated with each site, and (5) a REFERENCE file containing the bibliographic references. The files range in size from 2 to 66 kB.

PATSTAGS - PATRAN-STAGSC-1 TRANSLATOR

NASA Technical Reports Server (NTRS)

Otte, N. E.

1994-01-01

PATSTAGS translates PATRAN finite model data into STAGS (Structural Analysis of General Shells) input records to be used for engineering analysis. The program reads data from a PATRAN neutral file and writes STAGS input records into a STAGS input file and a UPRESS data file. It is able to support translations of nodal constraints, nodal, element, force and pressure data. PATSTAGS uses three files: the PATRAN neutral file to be translated, a STAGS input file and a STAGS pressure data file. The user provides the names for the neutral file and the desired names of the STAGS files to be created. The pressure data file contains the element live pressure data used in the STAGS subroutine UPRESS. PATSTAGS is written in FORTRAN 77 for DEC VAX series computers running VMS. The main memory requirement for execution is approximately 790K of virtual memory. Output blocks can be modified to output the data in any format desired, allowing the program to be used to translate model data to analysis codes other than STAGSC-1 (HQN-10967). This program is available in DEC VAX BACKUP format on a 9-track magnetic tape or TK50 tape cartridge. Documentation is included in the price of the program. PATSTAGS was developed in 1990. DEC, VAX, TK50 and VMS are trademarks of Digital Equipment Corporation.

Incorporating Brokers within Collaboration Environments

NASA Astrophysics Data System (ADS)

Rajasekar, A.; Moore, R.; de Torcy, A.

2013-12-01

A collaboration environment, such as the integrated Rule Oriented Data System (iRODS - http://irods.diceresearch.org), provides interoperability mechanisms for accessing storage systems, authentication systems, messaging systems, information catalogs, networks, and policy engines from a wide variety of clients. The interoperability mechanisms function as brokers, translating actions requested by clients to the protocol required by a specific technology. The iRODS data grid is used to enable collaborative research within hydrology, seismology, earth science, climate, oceanography, plant biology, astronomy, physics, and genomics disciplines. Although each domain has unique resources, data formats, semantics, and protocols, the iRODS system provides a generic framework that is capable of managing collaborative research initiatives that span multiple disciplines. Each interoperability mechanism (broker) is linked to a name space that enables unified access across the heterogeneous systems. The collaboration environment provides not only support for brokers, but also support for virtualization of name spaces for users, files, collections, storage systems, metadata, and policies. The broker enables access to data or information in a remote system using the appropriate protocol, while the collaboration environment provides a uniform naming convention for accessing and manipulating each object. Within the NSF DataNet Federation Consortium project (http://www.datafed.org), three basic types of interoperability mechanisms have been identified and applied: 1) drivers for managing manipulation at the remote resource (such as data subsetting), 2) micro-services that execute the protocol required by the remote resource, and 3) policies for controlling the execution. For example, drivers have been written for manipulating NetCDF and HDF formatted files within THREDDS servers. Micro-services have been written that manage interactions with the CUAHSI data repository, the DataONE information catalog, and the GeoBrain broker. Policies have been written that manage transfer of messages between an iRODS message queue and the Advanced Message Queuing Protocol. Examples of these brokering mechanisms will be presented. The DFC collaboration environment serves as the intermediary between community resources and compute grids, enabling reproducible data-driven research. It is possible to create an analysis workflow that retrieves data subsets from a remote server, assemble the required input files, automate the execution of the workflow, automatically track the provenance of the workflow, and share the input files, workflow, and output files. A collaborator can re-execute a shared workflow, compare results, change input files, and re-execute an analysis.

The development of method for continuous improvement of master file of the nursing practice terminology.

PubMed

Tsuru, Satoko; Okamine, Eiko; Takada, Aya; Watanabe, Chitose; Uchiyama, Makiko; Dannoue, Hideo; Aoyagi, Hisae; Endo, Akira

2009-01-01

Nursing Action Master and Nursing Observation Master were released from 2002 to 2008. Two kinds of format, an Excel format and a CSV format file are prepared for maintaining them. Followings were decided as a basic rule of the maintenance: newly addition, revision, deletion, the numbering of the management and a rule of the coding. The master was developed based on it. We do quality assurance for the masters using these rules.

PAnalyzer: a software tool for protein inference in shotgun proteomics.

PubMed

Prieto, Gorka; Aloria, Kerman; Osinalde, Nerea; Fullaondo, Asier; Arizmendi, Jesus M; Matthiesen, Rune

2012-11-05

Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

PAnalyzer: A software tool for protein inference in shotgun proteomics

PubMed Central

2012-01-01

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool. PMID:23126499

LONGLIB - A GRAPHICS LIBRARY

NASA Technical Reports Server (NTRS)

Long, D.

1994-01-01

This library is a set of subroutines designed for vector plotting to CRT's, plotters, dot matrix, and laser printers. LONGLIB subroutines are invoked by program calls similar to standard CALCOMP routines. In addition to the basic plotting routines, LONGLIB contains an extensive set of routines to allow viewport clipping, extended character sets, graphic input, shading, polar plots, and 3-D plotting with or without hidden line removal. LONGLIB capabilities include surface plots, contours, histograms, logarithm axes, world maps, and seismic plots. LONGLIB includes master subroutines, which are self-contained series of commonly used individual subroutines. When invoked, the master routine will initialize the plotting package, and will plot multiple curves, scatter plots, log plots, 3-D plots, etc. and then close the plot package, all with a single call. Supported devices include VT100 equipped with Selanar GR100 or GR100+ boards, VT125s, VT240s, VT220 equipped with Selanar SG220, Tektronix 4010/4014 or 4107/4109 and compatibles, and Graphon GO-235 terminals. Dot matrix printer output is available by using the provided raster scan conversion routines for DEC LA50, Printronix printers, and high or low resolution Trilog printers. Other output devices include QMS laser printers, Postscript compatible laser printers, and HPGL compatible plotters. The LONGLIB package includes the graphics library source code, an on-line help library, scan converter and meta file conversion programs, and command files for installing, creating, and testing the library. The latest version, 5.0, is significantly enhanced and has been made more portable. Also, the new version's meta file format has been changed and is incompatible with previous versions. A conversion utility is included to port the old meta files to the new format. Color terminal plotting has been incorporated. LONGLIB is written in FORTRAN 77 for batch or interactive execution and has been implemented on a DEC VAX series computer operating under VMS. This program was developed in 1985, and last updated in 1988.

Chapter 6. Tabular data and graphical images in support of the U.S. Geological Survey National Oil and Gas Assessment-East Texas basin and Louisiana-Mississippi salt basins provinces, Jurassic Smackover interior salt basins total petroleum system (504902), Travis Peak and Hosston formations.

USGS Publications Warehouse

,

2006-01-01

This chapter describes data used in support of the process being applied by the U.S. Geological Survey (USGS) National Oil and Gas Assessment (NOGA) project. Digital tabular data used in this report and archival data that permit the user to perform further analyses are available elsewhere on the CD-ROM. Computers and software may import the data without transcription from the Portable Document Format files (.pdf files) of the text by the reader. Because of the number and variety of platforms and software available, graphical images are provided as .pdf files and tabular data are provided in a raw form as tab-delimited text files (.tab files).

75 FR 71625 - System Restoration Reliability Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-24

... processing software should be filed in native applications or print-to-PDF format, and not in a scanned... (2006), aff'd sub nom. Alcoa, Inc. v. FERC, 564 F.3d 1342 (D.C. Cir. 2009). 6. On March 16, 2007, the... electronically using word processing software should be filed in native applications or print-to-PDF format, and...

75 FR 81152 - Interpretation of Protection System Reliability Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-27

... created electronically using word processing software should be filed in native applications or print-to... reh'g & compliance, 117 FERC ] 61,126 (2006), aff'd sub nom. Alcoa, Inc. v. FERC, 564 F.3d 1342 (DC... print-to-PDF format and not in a scanned format, at http://www.ferc.gov/docs-filing/efiling.asp . Mail...

78 FR 4766 - Adoption of Updated EDGAR Filer Manual

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-23

... primarily to introduce the new EDGARLink Online submission type IRANNOTICE; and support PDF as an official... Portable Document Format (PDF) as an official filing format. EDGAR will continue to accept ASCII and HTML...) and 101 (17 CFR 232.101) of Regulation S-T and the EDGAR Filer Manual relating to the use of PDF files...

75 FR 80296 - Extension of Filing Accommodation for Static Pool Information in Filings With Respect to Asset...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-22

... Systems in 1993 for document exchange. PDF captures formatting information from a variety of desktop publishing applications, making it possible to send formatted documents and have them appear on the recipient... Administrative Procedure Act generally requires that an agency publish an adopted rule in the Federal Register 30...

The NCAR Research Data Archive's Hybrid Approach for Data Discovery and Access

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2013-12-01

The NCAR Research Data Archive (RDA http://rda.ucar.edu) maintains a variety of data discovery and access capabilities for it's 600+ dataset collections to support the varying needs of a diverse user community. In-house developed and standards-based community tools offer services to more than 10,000 users annually. By number of users the largest group is external and access the RDA through web based protocols; the internal NCAR HPC users are fewer in number, but typically access more data volume. This paper will detail the data discovery and access services maintained by the RDA to support both user groups, and show metrics that illustrate how the community is using the services. The distributed search capability enabled by standards-based community tools, such as Geoportal and an OAI-PMH access point that serves multiple metadata standards, provide pathways for external users to initially discover RDA holdings. From here, in-house developed web interfaces leverage primary discovery level metadata databases that support keyword and faceted searches. Internal NCAR HPC users, or those familiar with the RDA, may go directly to the dataset collection of interest and refine their search based on rich file collection metadata. Multiple levels of metadata have proven to be invaluable for discovery within terabyte-sized archives composed of many atmospheric or oceanic levels, hundreds of parameters, and often numerous grid and time resolutions. Once users find the data they want, their access needs may vary as well. A THREDDS data server running on targeted dataset collections enables remote file access through OPENDAP and other web based protocols primarily for external users. In-house developed tools give all users the capability to submit data subset extraction and format conversion requests through scalable, HPC based delayed mode batch processing. Users can monitor their RDA-based data processing progress and receive instructions on how to access the data when it is ready. External users are provided with RDA server generated scripts to download the resulting request output. Similarly they can download native dataset collection files or partial files using Wget or cURL based scripts supplied by the RDA server. Internal users can access the resulting request output or native dataset collection files directly from centralized file systems.

Extending DIRAC File Management with Erasure-Coding for efficient storage.

NASA Astrophysics Data System (ADS)

Cadellin Skipsey, Samuel; Todev, Paulin; Britton, David; Crooks, David; Roy, Gareth

2015-12-01

The state of the art in Grid style data management is to achieve increased resilience of data via multiple complete replicas of data files across multiple storage endpoints. While this is effective, it is not the most space-efficient approach to resilience, especially when the reliability of individual storage endpoints is sufficiently high that only a few will be inactive at any point in time. We report on work performed as part of GridPP[1], extending the Dirac File Catalogue and file management interface to allow the placement of erasure-coded files: each file distributed as N identically-sized chunks of data striped across a vector of storage endpoints, encoded such that any M chunks can be lost and the original file can be reconstructed. The tools developed are transparent to the user, and, as well as allowing up and downloading of data to Grid storage, also provide the possibility of parallelising access across all of the distributed chunks at once, improving data transfer and IO performance. We expect this approach to be of most interest to smaller VOs, who have tighter bounds on the storage available to them, but larger (WLCG) VOs may be interested as their total data increases during Run 2. We provide an analysis of the costs and benefits of the approach, along with future development and implementation plans in this area. In general, overheads for multiple file transfers provide the largest issue for competitiveness of this approach at present.

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

PubMed

Bergmann, Frank T; Adams, Richard; Moodie, Stuart; Cooper, Jonathan; Glont, Mihai; Golebiewski, Martin; Hucka, Michael; Laibe, Camille; Miller, Andrew K; Nickerson, David P; Olivier, Brett G; Rodriguez, Nicolas; Sauro, Herbert M; Scharm, Martin; Soiland-Reyes, Stian; Waltemath, Dagmar; Yvon, Florent; Le Novère, Nicolas

2014-12-14

With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.

Tackling the 2nd V: Big Data, Variety and the Need for Representation Consistency

NASA Astrophysics Data System (ADS)

Clune, T.; Kuo, K. S.

2016-12-01

While Big Data technologies are transforming our ability to analyze ever larger volumes of Earth science data, practical constraints continue to limit our ability to compare data across datasets from different sources in an efficient and robust manner. Within a single data collection, invariants such as file format, grid type, and spatial resolution greatly simplify many types of analysis (often implicitly). However, when analysis combines data across multiple data collections, researchers are generally required to implement data transformations (i.e., "data preparation") to provide appropriate invariants. These transformation include changing of file formats, ingesting into a database, and/or regridding to a common spatial representation, and they can either be performed once, statically, or each time the data is accessed. At the very least, this process is inefficient from the perspective of the community as each team selects its own representation and privately implements the appropriate transformations. No doubt there are disadvantages to any "universal" representation, but we posit that major benefits would be obtained if a suitably flexible spatial representation could be standardized along with tools for transforming to/from that representation. We regard this as part of the historic trend in data publishing. Early datasets used ad hoc formats and lacked metadata. As better tools evolved, published data began to use standardized formats (e.g., HDF and netCDF) with attached metadata. We propose that the modern need to perform analysis across data sets should drive a new generation of tools that support a standardized spatial representation. More specifically, we propose the hierarchical triangular mesh (HTM) as a suitable "generic" resolution that permits standard transformations to/from native representations in use today, as well as tools to convert/regrid existing datasets onto that representation.

Digital map data, text, and graphical images in support of the 1995 National assessment of United States oil and gas resources

USGS Publications Warehouse

Beeman, William R.; Obuch, Raymond C.; Brewton, James D.

1996-01-01

This CD-ROM contains files in support of the 1995 USGS National assessment of United States oil and gas resources (DDS-30), which was published separately and summarizes the results of a 3-year study of the oil and gas resources of the onshore and state waters of the United States. The study describes about 560 oil and gas plays in the United States--confirmed and hypothetical, conventional and unconventional. A parallel study of the Federal offshore is being conducted by the U.S. Minerals Management Service. This CD-ROM contains files in multiple formats, so that almost any computer user can import them into word processors and mapping software packages. No proprietary data are released on this CD-ROM. The complete text of DDS-30 is also available, as well as many figures. A companion CD-ROM (DDS-36) includes the tabular data, the programs, and the same text data, but none of the map data.

Comparative analysis of data base management systems

NASA Technical Reports Server (NTRS)

Smith, R.

1983-01-01

A study to determine if the Remote File Inquiry (RFI) system would handle the future requirements of the user community is discussed. RFI is a locally written and locally maintained on-line query/update package. The current and future on-line requirements of the user community were studied. Additional consideration was given to the types of data structuring the users required. The survey indicated the features of greatest benefit were: sort, subtotals, totals, record selection, storage of queries, global updating and the ability to page break. The major deficiencies were: one level of hierarchy, excessive response time, software unreliability, difficult to add, delete and modify records, complicated error messages and the lack of ability to perform interfield comparisons. Missing features users required were: formatted screens, interfield comparions, interfield arithmetic, multiple file access, security and data integrity. The survey team recommended Kennedy Space Center move forward to state-of-the-art software, a Data Base Management System which is thoroughly tested and easy to implement and use.

A comparison of data interoperability approaches of fusion codes with application to synthetic diagnostics

NASA Astrophysics Data System (ADS)

Kruger, Scott; Shasharina, S.; Vadlamani, S.; McCune, D.; Holland, C.; Jenkins, T. G.; Candy, J.; Cary, J. R.; Hakim, A.; Miah, M.; Pletzer, A.

2010-11-01

As various efforts to integrate fusion codes proceed worldwide, standards for sharing data have emerged. In the U.S., the SWIM project has pioneered the development of the Plasma State, which has a flat-hierarchy and is dominated by its use within 1.5D transport codes. The European Integrated Tokamak Modeling effort has developed a more ambitious data interoperability effort organized around the concept of Consistent Physical Objects (CPOs). CPOs have deep hierarchies as needed by an effort that seeks to encompass all of fusion computing. Here, we discuss ideas for implementing data interoperability that is complementary to both the Plasma State and CPOs. By making use of attributes within the netcdf and HDF5 binary file formats, the goals of data interoperability can be achieved with a more informal approach. In addition, a file can be simultaneously interoperable to several standards at once. As an illustration of this approach, we discuss its application to the development of synthetic diagnostics that can be used for multiple codes.

Petroleum system modeling of the western Canada sedimentary basin - isopach grid files

USGS Publications Warehouse

Higley, Debra K.; Henry, Mitchell E.; Roberts, Laura N.R.

2005-01-01

This publication contains zmap-format grid files of isopach intervals that represent strata associated with Devonian to Holocene petroleum systems of the Western Canada Sedimentary Basin (WCSB) of Alberta, British Columbia, and Saskatchewan, Canada. Also included is one grid file that represents elevations relative to sea level of the top of the Lower Cretaceous Mannville Group. Vertical and lateral scales are in meters. The age range represented by the stratigraphic intervals comprising the grid files is 373 million years ago (Ma) to present day. File names, age ranges, formation intervals, and primary petroleum system elements are listed in table 1. Metadata associated with this publication includes information on the study area and the zmap-format files. The digital files listed in table 1 were compiled as part of the Petroleum Processes Research Project being conducted by the Central Energy Resources Team of the U.S. Geological Survey, which focuses on modeling petroleum generation, 3 migration, and accumulation through time for petroleum systems of the WCSB. Primary purposes of the WCSB study are to Construct the 1-D/2-D/3-D petroleum system models of the WCSB. Actual boundaries of the study area are documented within the metadata; excluded are northern Alberta and eastern Saskatchewan, but fringing areas of the United States are included.Publish results of the research and the grid files generated for use in the 3-D model of the WCSB.Evaluate the use of petroleum system modeling in assessing undiscovered oil and gas resources for geologic provinces across the World.

SEDIMENT DATA - ST. PAUL WATERWAY - TACOMA, WA - 1996 MONITORING DATA

EPA Science Inventory

Benthic Infauna Monitoring Data Files are Excel-format spreadsheet files which contain data presented in the St. Paul Waterway Area Remedial Action and Habitat Restoration Project, 1996 Monitoring Report. The files can be viewed directly or readily downlo aded and read into most ...

Active Management of Integrated Geothermal-CO2 Storage Reservoirs in Sedimentary Formations

DOE Data Explorer

Buscheck, Thomas A.

2012-01-01

Active Management of Integrated Geothermal–CO2 Storage Reservoirs in Sedimentary Formations: An Approach to Improve Energy Recovery and Mitigate Risk : FY1 Final Report The purpose of phase 1 is to determine the feasibility of integrating geologic CO2 storage (GCS) with geothermal energy production. Phase 1 includes reservoir analyses to determine injector/producer well schemes that balance the generation of economically useful flow rates at the producers with the need to manage reservoir overpressure to reduce the risks associated with overpressure, such as induced seismicity and CO2 leakage to overlying aquifers. This submittal contains input and output files of the reservoir model analyses. A reservoir-model "index-html" file was sent in a previous submittal to organize the reservoir-model input and output files according to sections of the FY1 Final Report to which they pertain. The recipient should save the file: Reservoir-models-inputs-outputs-index.html in the same directory that the files: Section2.1.*.tar.gz files are saved in.

Active Management of Integrated Geothermal-CO2 Storage Reservoirs in Sedimentary Formations

DOE Data Explorer

Buscheck, Thomas A.

2000-01-01

Active Management of Integrated Geothermal–CO2 Storage Reservoirs in Sedimentary Formations: An Approach to Improve Energy Recovery and Mitigate Risk: FY1 Final Report The purpose of phase 1 is to determine the feasibility of integrating geologic CO2 storage (GCS) with geothermal energy production. Phase 1 includes reservoir analyses to determine injector/producer well schemes that balance the generation of economically useful flow rates at the producers with the need to manage reservoir overpressure to reduce the risks associated with overpressure, such as induced seismicity and CO2 leakage to overlying aquifers. This submittal contains input and output files of the reservoir model analyses. A reservoir-model "index-html" file was sent in a previous submittal to organize the reservoir-model input and output files according to sections of the FY1 Final Report to which they pertain. The recipient should save the file: Reservoir-models-inputs-outputs-index.html in the same directory that the files: Section2.1.*.tar.gz files are saved in.

Parser Combinators: a Practical Application for Generating Parsers for NMR Data

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Ellis, Heidi JC; Gryk, Michael R.

2013-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy is a technique for acquiring protein data at atomic resolution and determining the three-dimensional structure of large protein molecules. A typical structure determination process results in the deposition of a large data sets to the BMRB (Bio-Magnetic Resonance Data Bank). This data is stored and shared in a file format called NMR-Star. This format is syntactically and semantically complex making it challenging to parse. Nevertheless, parsing these files is crucial to applying the vast amounts of biological information stored in NMR-Star files, allowing researchers to harness the results of previous studies to direct and validate future work. One powerful approach for parsing files is to apply a Backus-Naur Form (BNF) grammar, which is a high-level model of a file format. Translation of the grammatical model to an executable parser may be automatically accomplished. This paper will show how we applied a model BNF grammar of the NMR-Star format to create a free, open-source parser, using a method that originated in the functional programming world known as “parser combinators”. This paper demonstrates the effectiveness of a principled approach to file specification and parsing. This paper also builds upon our previous work [1], in that 1) it applies concepts from Functional Programming (which is relevant even though the implementation language, Java, is more mainstream than Functional Programming), and 2) all work and accomplishments from this project will be made available under standard open source licenses to provide the community with the opportunity to learn from our techniques and methods. PMID:24352525

VizieR Online Data Catalog: Infrared Arcturus Atlas (Hinkle+ 1995)

NASA Astrophysics Data System (ADS)

Hinkle, K.; Wallace, L.; Livingston, W.

1996-01-01

The atlas is contained in 310 spectral files a list of line identifications, plus a file containing a list of the files and unobserved spectral regions. The spectral file names are in the form 'abnnnnn' where 'nnnnn' denotes the spectral region, e.g. file 'ab4300' contains spectra for the 4300-4325 cm-1 range. The atomic and molecular line identifications are in files 'appendix.a' and 'appendix.b', and repeated with a uniform format in file 'lines'. The file 'appendix.c' is a book-keeping device used to correlate the plot plages and spectral files with frequency. See the author-supplied description in 'readme.dat' for more information. (311 data files).

Large File Transfers from Space Using Multiple Ground Terminals and Delay-Tolerant Networking

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Paulsen, Phillip; Stewart, Dave; Eddy, Wesley; McKim, James; Taylor, John; Lynch, Scott; Heberle, Jay; Northam, James; Jackson, Chris;

Hydratools, a MATLAB® based data processing package for Sontek Hydra data

USGS Publications Warehouse

Martini, M.; Lightsom, F.L.; Sherwood, C.R.; Xu, Jie; Lacy, J.R.; Ramsey, A.; Horwitz, R.

2005-01-01

The U.S. Geological Survey (USGS) has developed a set of MATLAB tools to process and convert data collected by Sontek Hydra instruments to netCDF, which is a format used by the USGS to process and archive oceanographic time-series data. The USGS makes high-resolution current measurements within 1.5 meters of the bottom. These data are used in combination with other instrument data from sediment transport studies to develop sediment transport models. Instrument manufacturers provide software which outputs unique binary data formats. Multiple data formats are cumbersome. The USGS solution is to translate data streams into a common data format: netCDF. The Hydratools toolbox is written to create netCDF format files following EPIC conventions, complete with embedded metadata. Data are accepted from both the ADV and the PCADP. The toolbox will detect and remove bad data, substitute other sources of heading and tilt measurements if necessary, apply ambiguity corrections, calculate statistics, return information about data quality, and organize metadata. Standardized processing and archiving makes these data more easily and routinely accessible locally and over the Internet. In addition, documentation of the techniques used in the toolbox provides a baseline reference for others utilizing the data.

Geologic map of the Valjean Hills 7.5' quadrangle, San Bernardino County, California

USGS Publications Warehouse

Calzia, J.P.; Troxel, Bennie W.; digital database by Raumann, Christian G.

2003-01-01

FGDC-compliant metadata for the ARC/INFO coverages. The Correlation of Map Units and Description of Map Units is in the editorial format of USGS Geologic Investigations Series (I-series) maps but has not been edited to comply with I-map standards. Within the geologic map data package, map units are identified by standard geologic map criteria such as formation-name, age, and lithology. Even though this is an Open-File Report and includes the standard USGS Open-File disclaimer, the report closely adheres to the stratigraphic nomenclature of the U.S. Geological Survey. Descriptions of units can be obtained by viewing or plotting the .pdf file (3 above) or plotting the postscript file (2 above).

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

CSAM: Compressed SAM format.

PubMed

Cánovas, Rodrigo; Moffat, Alistair; Turpin, Andrew

2016-12-15

Next generation sequencing machines produce vast amounts of genomic data. For the data to be useful, it is essential that it can be stored and manipulated efficiently. This work responds to the combined challenge of compressing genomic data, while providing fast access to regions of interest, without necessitating decompression of whole files. We describe CSAM (Compressed SAM format), a compression approach offering lossless and lossy compression for SAM files. The structures and techniques proposed are suitable for representing SAM files, as well as supporting fast access to the compressed information. They generate more compact lossless representations than BAM, which is currently the preferred lossless compressed SAM-equivalent format; and are self-contained, that is, they do not depend on any external resources to compress or decompress SAM files. An implementation is available at https://github.com/rcanovas/libCSAM CONTACT: canovas-ba@lirmm.frSupplementary Information: Supplementary data is available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Software for Automated Reading of STEP Files by I-DEAS(trademark)

NASA Technical Reports Server (NTRS)

Pinedo, John

2003-01-01

A program called "readstep" enables the I-DEAS(tm) computer-aided-design (CAD) software to automatically read Standard for the Exchange of Product Model Data (STEP) files. (The STEP format is one of several used to transfer data between dissimilar CAD programs.) Prior to the development of "readstep," it was necessary to read STEP files into I-DEAS(tm) one at a time in a slow process that required repeated intervention by the user. In operation, "readstep" prompts the user for the location of the desired STEP files and the names of the I-DEAS(tm) project and model file, then generates an I-DEAS(tm) program file called "readstep.prg" and two Unix shell programs called "runner" and "controller." The program "runner" runs I-DEAS(tm) sessions that execute readstep.prg, while "controller" controls the execution of "runner" and edits readstep.prg if necessary. The user sets "runner" and "controller" into execution simultaneously, and then no further intervention by the user is required. When "runner" has finished, the user should see only parts from successfully read STEP files present in the model file. STEP files that could not be read successfully (e.g., because of format errors) should be regenerated before attempting to read them again.

Shuttle Data Center File-Processing Tool in Java

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Miller, Walter H.

2006-01-01

A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

Users' Manual and Installation Guide for the EverVIEW Slice and Dice Tool (Version 1.0 Beta)

USGS Publications Warehouse

Roszell, Dustin; Conzelmann, Craig; Chimmula, Sumani; Chandrasekaran, Anuradha; Hunnicut, Christina

2009-01-01

Network Common Data Form (NetCDF) is a self-describing, machine-independent file format for storing array-oriented scientific data. Over the past few years, there has been a growing movement within the community of natural resource managers in The Everglades, Fla., to use NetCDF as the standard data container for datasets based on multidimensional arrays. As a consequence, a need arose for additional tools to view and manipulate NetCDF datasets, specifically to create subsets of large NetCDF files. To address this need, we created the EverVIEW Slice and Dice Tool to allow users to create subsets of grid-based NetCDF files. The major functions of this tool are (1) to subset NetCDF files both spatially and temporally; (2) to view the NetCDF data in table form; and (3) to export filtered data to a comma-separated value file format.

HDF4 Maps: For Now and For the Future

NASA Astrophysics Data System (ADS)

Plutchak, J.; Aydt, R.; Folk, M. J.

2013-12-01

Data formats and access tools necessarily change as technology improves to address emerging requirements with new capabilities. This on-going process inevitably leaves behind significant data collections in legacy formats that are difficult to support and sustain. NASA ESDIS and The HDF Group currently face this problem with large and growing archives of data in HDF4, an older version of the HDF format. Indefinitely guaranteeing the ability to read these data with multi-platform libraries in many languages is very difficult. As an alternative, HDF and NASA worked together to create maps of the files that contain metadata and information about data types, locations, and sizes of data objects in the files. These maps are written in XML and have successfully been used to access and understand data in HDF4 files without the HDF libraries. While originally developed to support sustainable access to these data, these maps can also be used to provide access to HDF4 metadata, facilitate user understanding of files prior to download, and validate the files for compliance with particular conventions. These capabilities are now available as a service for HDF4 archives and users.

75 FR 57327 - GNP Rly, Inc.-Acquisition and Operation Exemption-Redmond Spur and Woodinville Subdivision

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-20

...). Those NITUs permitted railbanking/interim trail use negotiations under the Trails Act, 16 U.S.C. 1247(d... November 19, 2010. ADDRESSES: Comments may be submitted either via the Board's e-filing format or in the traditional paper format. Any person using e-filing should attach a document and otherwise comply with the...

MITRE sensor layer prototype

NASA Astrophysics Data System (ADS)

Duff, Francis; McGarry, Donald; Zasada, David; Foote, Scott

2009-05-01

The MITRE Sensor Layer Prototype is an initial design effort to enable every sensor to help create new capabilities through collaborative data sharing. By making both upstream (raw) and downstream (processed) sensor data visible, users can access the specific level, type, and quantities of data needed to create new data products that were never anticipated by the original designers of the individual sensors. The major characteristic that sets sensor data services apart from typical enterprise services is the volume (on the order of multiple terabytes) of raw data that can be generated by most sensors. Traditional tightly coupled processing approaches extract pre-determined information from the incoming raw sensor data, format it, and send it to predetermined users. The community is rapidly reaching the conclusion that tightly coupled sensor processing loses too much potentially critical information.1 Hence upstream (raw and partially processed) data must be extracted, rapidly archived, and advertised to the enterprise for unanticipated uses. The authors believe layered sensing net-centric integration can be achieved through a standardize-encapsulate-syndicateaggregate- manipulate-process paradigm. The Sensor Layer Prototype's technical approach focuses on implementing this proof of concept framework to make sensor data visible, accessible and useful to the enterprise. To achieve this, a "raw" data tap between physical transducers associated with sensor arrays and the embedded sensor signal processing hardware and software has been exploited. Second, we encapsulate and expose both raw and partially processed data to the enterprise within the context of a service-oriented architecture. Third, we advertise the presence of multiple types, and multiple layers of data through geographic-enabled Really Simple Syndication (GeoRSS) services. These GeoRSS feeds are aggregated, manipulated, and filtered by a feed aggregator. After filtering these feeds to bring just the type and location of data sought by multiple processes to the attention of each processing station, just that specifically sought data is downloaded to each process application. The Sensor Layer Prototype participated in a proof-of-concept demonstration in April 2008. This event allowed multiple MITRE innovation programs to interact among themselves to demonstrate the ability to couple value-adding but previously unanticipated users to the enterprise. For this event, the Sensor Layer Prototype was used to show data entering the environment in real time. Multiple data types were encapsulated and added to the database via the Sensor Layer Prototype, specifically National Imagery Transmission Format 2.1 (NITF), NATO Standardization Format 4607 (STANAG 4607), Cursor-on-Target (CoT), Joint Photographic Experts Group (JPEG), Hierarchical Data Format (HDF5) and several additional sensor file formats describing multiple sensors addressing a common scenario.

Challenges to Standardization: A Case Study Using Coastal and Deep-Ocean Water Level Data

NASA Astrophysics Data System (ADS)

Sweeney, A. D.; Stroker, K. J.; Mungov, G.; McLean, S. J.

2015-12-01

Sea levels recorded at coastal stations and inferred from deep-ocean pressure observations at the seafloor are submitted for archive in multiple data and metadata formats. These formats include two forms of schema-less XML and a custom binary format accompanied by metadata in a spreadsheet. The authors report on efforts to use existing standards to make this data more discoverable and more useful beyond their initial use in detecting tsunamis. An initial review of data formats for sea level data around the globe revealed heterogeneity in presentation and content. In the absence of a widely-used domain-specific format, we adopted the general model for structuring data and metadata expressed by the Network Common Data Form (netCDF). netCDF has been endorsed by the Open Geospatial Consortium and has the advantages of small size when compared to equivalent plain text representation and provides a standard way of embedding metadata in the same file. We followed the orthogonal time-series profile of the Climate and Forecast discrete sampling geometries as the convention for structuring the data and describing metadata relevant for use. We adhered to the Attribute Convention for Data Discovery for capturing metadata to support user search. Beyond making it possible to structure data and metadata in a standard way, netCDF is supported by multiple software tools in providing programmatic cataloging, access, subsetting, and transformation to other formats. We will describe our successes and failures in adhering to existing standards and provide requirements for either augmenting existing conventions or developing new ones. Some of these enhancements are specific to sea level data, while others are applicable to time-series data in general.

FastStats: Obstetrical Procedures

MedlinePlus

... Publications and Information Products Surveys and Data Collection Systems Washington Group on Disability Statistics Where to Write for Vital Records File Formats Help: How do I view different file ...

FastStats: Prostate Disease

MedlinePlus

... Publications and Information Products Surveys and Data Collection Systems Washington Group on Disability Statistics Where to Write for Vital Records File Formats Help: How do I view different file ...

BOREAS RSS-8 BIOME-BGC Model Simulations at Tower Flux Sites in 1994

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Nickeson, Jaime (Editor); Kimball, John

2000-01-01

BIOME-BGC is a general ecosystem process model designed to simulate biogeochemical and hydrologic processes across multiple scales (Running and Hunt, 1993). In this investigation, BIOME-BGC was used to estimate daily water and carbon budgets for the BOREAS tower flux sites for 1994. Carbon variables estimated by the model include gross primary production (i.e., net photosynthesis), maintenance and heterotrophic respiration, net primary production, and net ecosystem carbon exchange. Hydrologic variables estimated by the model include snowcover, evaporation, transpiration, evapotranspiration, soil moisture, and outflow. The information provided by the investigation includes input initialization and model output files for various sites in tabular ASCII format.

HepML, an XML-based format for describing simulated data in high energy physics

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

2010-10-01

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces - Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size - 25.0 Kb).

BOREAS Forest Cover Data Layers over the SSA-MSA in Raster Format

NASA Technical Reports Server (NTRS)

Nickeson, Jaime; Gruszka, F; Hall, F.

2000-01-01

This data set, originally provided as vector polygons with attributes, has been processed by BORIS staff to provide raster files that can be used for modeling or for comparison purposes. The original data were received as ARC/INFO coverages or as export files from SERM. The data include information on forest parameters for the BOREAS SSA-MSA. Most of the data used for this product were acquired by BORIS in 1993; the maps were produced from aerial photography taken as recently as 1988. The data are stored in binary, image format files.

UNICON: A Powerful and Easy-to-Use Compound Library Converter.

PubMed

Sommer, Kai; Friedrich, Nils-Ole; Bietz, Stefan; Hilbig, Matthias; Inhester, Therese; Rarey, Matthias

2016-06-27

The accurate handling of different chemical file formats and the consistent conversion between them play important roles for calculations in complex cheminformatics workflows. Working with different cheminformatic tools often makes the conversion between file formats a mandatory step. Such a conversion might become a difficult task in cases where the information content substantially differs. This paper describes UNICON, an easy-to-use software tool for this task. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, PDB, and PDBx/mmCIF via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states, and conformer ensembles. For this purpose, UNICON bundles the key elements of the previously described NAOMI library in a single, easy-to-use command line tool.

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

iPat: intelligent prediction and association tool for genomic research.

PubMed

Chen, Chunpeng James; Zhang, Zhiwu

2018-06-01

The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills. Non-programmers struggle to use them efficiently because of the steep learning curves and zero tolerance for data formats and mistakes when inputting keywords and parameters. To address these problems, this study developed a software package, named the Intelligent Prediction and Association Tool (iPat), with a user-friendly graphical user interface. With iPat, GWAS or GS can be performed using a pointing device to simply drag and/or click on graphical elements to specify input data files, choose input parameters and select analytical models. Models available to users include those implemented in third party CLI packages such as GAPIT, PLINK, FarmCPU, BLINK, rrBLUP and BGLR. Users can choose any data format and conduct analyses with any of these packages. File conversions are automatically conducted for specified input data and selected packages. A GWAS-assisted genomic prediction method was implemented to perform genomic prediction using any GWAS method such as FarmCPU. iPat was written in Java for adaptation to multiple operating systems including Windows, Mac and Linux. The iPat executable file, user manual, tutorials and example datasets are freely available at http://zzlab.net/iPat. zhiwu.zhang@wsu.edu.

morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python

PubMed Central

Hull, Michael J.; Willshaw, David J.

2014-01-01

The broad structure of a modeling study can often be explained over a cup of coffee, but converting this high-level conceptual idea into graphs of the final simulation results may require many weeks of sitting at a computer. Although models themselves can be complex, often many mental resources are wasted working around complexities of the software ecosystem such as fighting to manage files, interfacing between tools and data formats, finding mistakes in code or working out the units of variables. morphforge is a high-level, Python toolbox for building and managing simulations of small populations of multicompartmental biophysical model neurons. An entire in silico experiment, including the definition of neuronal morphologies, channel descriptions, stimuli, visualization and analysis of results can be written within a single short Python script using high-level objects. Multiple independent simulations can be created and run from a single script, allowing parameter spaces to be investigated. Consideration has been given to the reuse of both algorithmic and parameterizable components to allow both specific and stochastic parameter variations. Some other features of the toolbox include: the automatic generation of human-readable documentation (e.g., PDF files) about a simulation; the transparent handling of different biophysical units; a novel mechanism for plotting simulation results based on a system of tags; and an architecture that supports both the use of established formats for defining channels and synapses (e.g., MODL files), and the possibility to support other libraries and standards easily. We hope that this toolbox will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development. PMID:24478690

Java Library for Input and Output of Image Data and Metadata

NASA Technical Reports Server (NTRS)

Deen, Robert; Levoe, Steven

2003-01-01

A Java-language library supports input and output (I/O) of image data and metadata (label data) in the format of the Video Image Communication and Retrieval (VICAR) image-processing software and in several similar formats, including a subset of the Planetary Data System (PDS) image file format. The library does the following: It provides low-level, direct access layer, enabling an application subprogram to read and write specific image files, lines, or pixels, and manipulate metadata directly. Two coding/decoding subprograms ("codecs" for short) based on the Java Advanced Imaging (JAI) software provide access to VICAR and PDS images in a file-format-independent manner. The VICAR and PDS codecs enable any program that conforms to the specification of the JAI codec to use VICAR or PDS images automatically, without specific knowledge of the VICAR or PDS format. The library also includes Image I/O plugin subprograms for VICAR and PDS formats. Application programs that conform to the Image I/O specification of Java version 1.4 can utilize any image format for which such a plug-in subprogram exists, without specific knowledge of the format itself. Like the aforementioned codecs, the VICAR and PDS Image I/O plug-in subprograms support reading and writing of metadata.

A linked GeoData map for enabling information access

USGS Publications Warehouse

Powell, Logan J.; Varanka, Dalia E.

2018-01-10

OverviewThe Geospatial Semantic Web (GSW) is an emerging technology that uses the Internet for more effective knowledge engineering and information extraction. Among the aims of the GSW are to structure the semantic specifications of data to reduce ambiguity and to link those data more efficiently. The data are stored as triples, the basic data unit in graph databases, which are similar to the vector data model of geographic information systems (GIS); that is, a node-edge-node model that forms a graph of semantically related information. The GSW is supported by emerging technologies such as linked geospatial data, described below, that enable it to store and manage geographical data that require new cartographic methods for visualization. This report describes a map that can interact with linked geospatial data using a simulation of a data query approach called the browsable graph to find information that is semantically related to a subject of interest, visualized using the Data Driven Documents (D3) library. Such a semantically enabled map functions as a map knowledge base (MKB) (Varanka and Usery, 2017).A MKB differs from a database in an important way. The central element of a triple, alternatively called the edge or property, is composed of a logic formalization that structures the relation between the first and third parts, the nodes or objects. Node-edge-node represents the graphic form of the triple, and the subject-property-object terms represent the data structure. Object classes connect to build a federated graph, similar to a network in visual form. Because the triple property is a logical statement (a predicate), the data graph represents logical propositions or assertions accepted to be true about the subject matter. These logical formalizations can be manipulated to calculate new triples, representing inferred logical assertions, from the existing data.To demonstrate a MKB system, a technical proof-of-concept is developed that uses geographically attributed Resource Description Framework (RDF) serializations of linked data for mapping. The proof-of-concept focuses on accessing triple data from visual elements of a geographic map as the interface to the MKB. The map interface is embedded with other essential functions such as SPARQL Protocol and RDF Query Language (SPARQL) data query endpoint services and reasoning capabilities of Apache Marmotta (Apache Software Foundation, 2017). An RDF database of the Geographic Names Information System (GNIS), which contains official names of domestic feature in the United States, was linked to a county data layer from The National Map of the U.S. Geological Survey. The county data are part of a broader Government Units theme offered to the public as Esri shapefiles. The shapefile used to draw the map itself was converted to a geographic-oriented JavaScript Object Notation (JSON) (GeoJSON) format and linked through various properties with a linked geodata version of the GNIS database called “GNIS–LD” (Butler and others, 2016; B. Regalia and others, University of California-Santa Barbara, written commun., 2017). The GNIS–LD files originated in Terse RDF Triple Language (Turtle) format but were converted to a JSON format specialized in linked data, “JSON–LD” (Beckett and Berners-Lee, 2011; Sorny and others, 2014). The GNIS–LD database is composed of roughly three predominant triple data graphs: Features, Names, and History. The graphs include a set of namespace prefixes used by each of the attributes. Predefining the prefixes made the conversion to the JSON–LD format simple to complete because Turtle and JSON–LD are variant specifications of the basic RDF concept.To convert a shapefile into GeoJSON format to capture the geospatial coordinate geometry objects, an online converter, Mapshaper, was used (Bloch, 2013). To convert the Turtle files, a custom converter written in Java reconstructs the files by parsing each grouping of attributes belonging to one subject and pasting the data into a new file that follows the syntax of JSON–LD. Additionally, the Features file contained its own set of geometries, which was exported into a separate JSON–LD file along with its elevation value to form a fourth file, named “features-geo.json.” Extracted data from external files can be represented in HyperText Markup Language (HTML) path objects. The goal was to import multiple JSON–LD files using this approach.

Cambio : a file format translation and analysis application for the nuclear response emergency community.

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

Lasche, George P.

2009-10-01

Cambio is an application intended to automatically read and display any spectrum file of any format in the world that the nuclear emergency response community might encounter. Cambio also provides an analysis capability suitable for HPGe spectra when detector response and scattering environment are not well known. Why is Cambio needed: (1) Cambio solves the following problem - With over 50 types of formats from instruments used in the field and new format variations appearing frequently, it is impractical for every responder to have current versions of the manufacturer's software from every instrument used in the field; (2) Cambio convertsmore » field spectra to any one of several common formats that are used for analysis, saving valuable time in an emergency situation; (3) Cambio provides basic tools for comparing spectra, calibrating spectra, and isotope identification with analysis suited especially for HPGe spectra; and (4) Cambio has a batch processing capability to automatically translate a large number of archival spectral files of any format to one of several common formats, such as the IAEA SPE or the DHS N42. Currently over 540 analysts and members of the nuclear emergency response community worldwide are on the distribution list for updates to Cambio. Cambio users come from all levels of government, university, and commercial partners around the world that support efforts to counter terrorist nuclear activities. Cambio is Unclassified Unlimited Release (UUR) and distributed by internet downloads with email notifications whenever a new build of Cambio provides for new formats, bug fixes, or new or improved capabilities. Cambio is also provided as a DLL to the Karlsruhe Institute for Transuranium Elements so that Cambio's automatic file-reading capability can be included at the Nucleonica web site.« less

75 FR 41093 - FM Table of Allotments, Maupin, Oregon

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

.... SUMMARY: The Audio Division grants the Petition for Reconsideration filed on behalf of Maupin Broadcasting... materials in accessible formats for people with disabilities (Braille, large print, electronic files, audio.... John A. Karousos, Assistant Chief, Audio Division, Media Bureau. [FR Doc. 2010-17226 Filed 7-14-10; 8...

Quantitative Microbial Risk Assessment Tutorial: Publishing a Microbial Density Time Series as a Txt File

EPA Science Inventory

A SARA Timeseries Utility supports analysis and management of time-varying environmental data including listing, graphing, computing statistics, computing meteorological data and saving in a WDM or text file. File formats supported include WDM, HSPF Binary (.hbn), USGS RDB, and T...

Neutron Detector Signal Processing to Calculate the Effective Neutron Multiplication Factor of Subcritical Assemblies

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

Talamo, Alberto; Gohar, Yousry

2016-06-01

This report describes different methodologies to calculate the effective neutron multiplication factor of subcritical assemblies by processing the neutron detector signals using MATLAB scripts. The subcritical assembly can be driven either by a spontaneous fission neutron source (e.g. californium) or by a neutron source generated from the interactions of accelerated particles with target materials. In the latter case, when the particle accelerator operates in a pulsed mode, the signals are typically stored into two files. One file contains the time when neutron reactions occur and the other contains the times when the neutron pulses start. In both files, the timemore » is given by an integer representing the number of time bins since the start of the counting. These signal files are used to construct the neutron count distribution from a single neutron pulse. The built-in functions of MATLAB are used to calculate the effective neutron multiplication factor through the application of the prompt decay fitting or the area method to the neutron count distribution. If the subcritical assembly is driven by a spontaneous fission neutron source, then the effective multiplication factor can be evaluated either using the prompt neutron decay constant obtained from Rossi or Feynman distributions or the Modified Source Multiplication (MSM) method.« less

IDG - INTERACTIVE DIF GENERATOR

NASA Technical Reports Server (NTRS)

Preheim, L. E.

1994-01-01

The Interactive DIF Generator (IDG) utility is a tool used to generate and manipulate Directory Interchange Format files (DIF). Its purpose as a specialized text editor is to create and update DIF files which can be sent to NASA's Master Directory, also referred to as the International Global Change Directory at Goddard. Many government and university data systems use the Master Directory to advertise the availability of research data. The IDG interface consists of a set of four windows: (1) the IDG main window; (2) a text editing window; (3) a text formatting and validation window; and (4) a file viewing window. The IDG main window starts up the other windows and contains a list of valid keywords. The keywords are loaded from a user-designated file and selected keywords can be copied into any active editing window. Once activated, the editing window designates the file to be edited. Upon switching from the editing window to the formatting and validation window, the user has options for making simple changes to one or more files such as inserting tabs, aligning fields, and indenting groups. The viewing window is a scrollable read-only window that allows fast viewing of any text file. IDG is an interactive tool and requires a mouse or a trackball to operate. IDG uses the X Window System to build and manage its interactive forms, and also uses the Motif widget set and runs under Sun UNIX. IDG is written in C-language for Sun computers running SunOS. This package requires the X Window System, Version 11 Revision 4, with OSF/Motif 1.1. IDG requires 1.8Mb of hard disk space. The standard distribution medium for IDG is a .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format. The program was developed in 1991 and is a copyrighted work with all copyright vested in NASA. SunOS is a trademark of Sun Microsystems, Inc. X Window System is a trademark of Massachusetts Institute of Technology. OSF/Motif is a trademark of the Open Software Foundation, Inc. UNIX is a trademark of Bell Laboratories.

Hear it, See it, Explore it: Visualizations and Sonifications of Seismic Signals

NASA Astrophysics Data System (ADS)

Fisher, M.; Peng, Z.; Simpson, D. W.; Kilb, D. L.

2010-12-01

Sonification of seismic data is an innovative way to represent seismic data in the audible range (Simpson, 2005). Seismic waves with different frequency and temporal characteristics, such as those from teleseismic earthquakes, deep “non-volcanic” tremor and local earthquakes, can be easily discriminated when time-compressed to the audio range. Hence, sonification is particularly useful for presenting complicated seismic signals with multiple sources, such as aftershocks within the coda of large earthquakes, and remote triggering of earthquakes and tremor by large teleseismic earthquakes. Previous studies mostly focused on converting the seismic data into audible files by simple time compression or frequency modulation (Simpson et al., 2009). Here we generate animations of the seismic data together with the sounds. We first read seismic data in the SAC format into Matlab, and generate a sequence of image files and an associated WAV sound file. Next, we use a third party video editor, such as the QuickTime Pro, to combine the image sequences and the sound file into an animation. We have applied this simple procedure to generate animations of remotely triggered earthquakes, tremor and low-frequency earthquakes in California, and mainshock-aftershock sequences in Japan and California. These animations clearly demonstrate the interactions of earthquake sequences and the richness of the seismic data. The tool developed in this study can be easily adapted for use in other research applications and to create sonification/animation of seismic data for education and outreach purpose.

Performance of the Galley Parallel File System

NASA Technical Reports Server (NTRS)

Nieuwejaar, Nils; Kotz, David

1996-01-01

As the input/output (I/O) needs of parallel scientific applications increase, file systems for multiprocessors are being designed to provide applications with parallel access to multiple disks. Many parallel file systems present applications with a conventional Unix-like interface that allows the application to access multiple disks transparently. This interface conceals the parallism within the file system, which increases the ease of programmability, but makes it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. Furthermore, most current parallel file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic parallel workloads. Initial experiments, reported in this paper, indicate that Galley is capable of providing high-performance 1/O to applications the applications that rely on them. In Section 3 we describe that access data in patterns that have been observed to be common.

Mars Global Digital Dune Database: MC2-MC29

USGS Publications Warehouse

Hayward, Rosalyn K.; Mullins, Kevin F.; Fenton, L.K.; Hare, T.M.; Titus, T.N.; Bourke, M.C.; Colaprete, Anthony; Christensen, P.R.

2007-01-01

Introduction The Mars Global Digital Dune Database presents data and describes the methodology used in creating the database. The database provides a comprehensive and quantitative view of the geographic distribution of moderate- to large-size dune fields from 65? N to 65? S latitude and encompasses ~ 550 dune fields. The database will be expanded to cover the entire planet in later versions. Although we have attempted to include all dune fields between 65? N and 65? S, some have likely been excluded for two reasons: 1) incomplete THEMIS IR (daytime) coverage may have caused us to exclude some moderate- to large-size dune fields or 2) resolution of THEMIS IR coverage (100m/pixel) certainly caused us to exclude smaller dune fields. The smallest dune fields in the database are ~ 1 km2 in area. While the moderate to large dune fields are likely to constitute the largest compilation of sediment on the planet, smaller stores of sediment of dunes are likely to be found elsewhere via higher resolution data. Thus, it should be noted that our database excludes all small dune fields and some moderate to large dune fields as well. Therefore the absence of mapped dune fields does not mean that such dune fields do not exist and is not intended to imply a lack of saltating sand in other areas. Where availability and quality of THEMIS visible (VIS) or Mars Orbiter Camera narrow angle (MOC NA) images allowed, we classifed dunes and included dune slipface measurements, which were derived from gross dune morphology and represent the prevailing wind direction at the last time of significant dune modification. For dunes located within craters, the azimuth from crater centroid to dune field centroid was calculated. Output from a general circulation model (GCM) is also included. In addition to polygons locating dune fields, the database includes over 1800 selected Thermal Emission Imaging System (THEMIS) infrared (IR), THEMIS visible (VIS) and Mars Orbiter Camera Narrow Angle (MOC NA) images that were used to build the database. The database is presented in a variety of formats. It is presented as a series of ArcReader projects which can be opened using the free ArcReader software. The latest version of ArcReader can be downloaded at http://www.esri.com/software/arcgis/arcreader/download.html. The database is also presented in ArcMap projects. The ArcMap projects allow fuller use of the data, but require ESRI ArcMap? software. Multiple projects were required to accommodate the large number of images needed. A fuller description of the projects can be found in the Dunes_ReadMe file and the ReadMe_GIS file in the Documentation folder. For users who prefer to create their own projects, the data is available in ESRI shapefile and geodatabase formats, as well as the open Geographic Markup Language (GML) format. A printable map of the dunes and craters in the database is available as a Portable Document Format (PDF) document. The map is also included as a JPEG file. ReadMe files are available in PDF and ASCII (.txt) files. Tables are available in both Excel (.xls) and ASCII formats.

Tabular data, text, and graphical images in support of the 1995 National assessment of United States oil and gas resources

USGS Publications Warehouse

Charpentier, Ronald R.; Klett, T.R.; Obuch, R.C.; Brewton, J.D.

1996-01-01

This CD-ROM contains files in support of the 1995 USGS National assessment of United States oil and gas resources (DDS-30), which was published separately and summarizes the results of a 3-year study of the oil and gas resources of the onshore and state waters of the United States. The study describes about 560 oil and gas plays in the United States; confirmed and hypothetical, conventional and unconventional. A parallel study of the Federal offshore is being conducted by the U.S. Minerals Management Service. This CD-ROM contains files in multiple formats, so that almost any computer user can import them into word processors and spreadsheets. The tabular data include some tables not released in DDS-30. No proprietary data are released on this CD-ROM, but some tables of summary statistics from the proprietary files are provided. The complete text of DDS-30 is also available, as well as many figures. Also included are some of the programs used in the assessment, in source code and with supporting documentation. A companion CD-ROM (DDS-35) includes the map data and the same text data, but none of the tabular data or assessment programs.

Software system for data management and distributed processing of multichannel biomedical signals.

PubMed

Franaszczuk, P J; Jouny, C C

2004-01-01

The presented software is designed for efficient utilization of cluster of PC computers for signal analysis of multichannel physiological data. The system consists of three main components: 1) a library of input and output procedures, 2) a database storing additional information about location in a storage system, 3) a user interface for selecting data for analysis, choosing programs for analysis, and distributing computing and output data on cluster nodes. The system allows for processing multichannel time series data in multiple binary formats. The description of data format, channels and time of recording are included in separate text files. Definition and selection of multiple channel montages is possible. Epochs for analysis can be selected both manually and automatically. Implementation of a new signal processing procedures is possible with a minimal programming overhead for the input/output processing and user interface. The number of nodes in cluster used for computations and amount of storage can be changed with no major modification to software. Current implementations include the time-frequency analysis of multiday, multichannel recordings of intracranial EEG of epileptic patients as well as evoked response analyses of repeated cognitive tasks.

ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models.

PubMed

Marvel, Skylar W; To, Kimberly; Grimm, Fabian A; Wright, Fred A; Rusyn, Ivan; Reif, David M

2018-03-05

Drawing integrated conclusions from diverse source data requires synthesis across multiple types of information. The ToxPi (Toxicological Prioritization Index) is an analytical framework that was developed to enable integration of multiple sources of evidence by transforming data into integrated, visual profiles. Methodological improvements have advanced ToxPi and expanded its applicability, necessitating a new, consolidated software platform to provide functionality, while preserving flexibility for future updates. We detail the implementation of a new graphical user interface for ToxPi (Toxicological Prioritization Index) that provides interactive visualization, analysis, reporting, and portability. The interface is deployed as a stand-alone, platform-independent Java application, with a modular design to accommodate inclusion of future analytics. The new ToxPi interface introduces several features, from flexible data import formats (including legacy formats that permit backward compatibility) to similarity-based clustering to options for high-resolution graphical output. We present the new ToxPi interface for dynamic exploration, visualization, and sharing of integrated data models. The ToxPi interface is freely-available as a single compressed download that includes the main Java executable, all libraries, example data files, and a complete user manual from http://toxpi.org .

Managing hydrological measurements for small and intermediate projects: RObsDat

NASA Astrophysics Data System (ADS)

Reusser, Dominik E.

2014-05-01

Hydrological measurements need good management for the data not to be lost. Multiple, often overlapping files from various loggers with heterogeneous formats need to be merged. Data needs to be validated and cleaned and subsequently converted to the format for the hydrological target application. Preferably, all these steps should be easily tracable. RObsDat is an R package designed to support such data management. It comes with a command line user interface to support hydrologists to enter and adjust their data in a database following the Observations Data Model (ODM) standard by QUASHI. RObsDat helps in the setup of the database within one of the free database engines MySQL, PostgreSQL or SQLite. It imports the controlled water vocabulary from the QUASHI web service and provides a smart interface between the hydrologist and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designes to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. A new development is the use of spacetime objects for subsequent processing.

TIGER: Turbomachinery interactive grid generation

NASA Technical Reports Server (NTRS)

Soni, Bharat K.; Shih, Ming-Hsin; Janus, J. Mark

1992-01-01

A three dimensional, interactive grid generation code, TIGER, is being developed for analysis of flows around ducted or unducted propellers. TIGER is a customized grid generator that combines new technology with methods from general grid generation codes. The code generates multiple block, structured grids around multiple blade rows with a hub and shroud for either C grid or H grid topologies. The code is intended for use with a Euler/Navier-Stokes solver also being developed, but is general enough for use with other flow solvers. TIGER features a silicon graphics interactive graphics environment that displays a pop-up window, graphics window, and text window. The geometry is read as a discrete set of points with options for several industrial standard formats and NASA standard formats. Various splines are available for defining the surface geometries. Grid generation is done either interactively or through a batch mode operation using history files from a previously generated grid. The batch mode operation can be done either with a graphical display of the interactive session or with no graphics so that the code can be run on another computer system. Run time can be significantly reduced by running on a Cray-YMP.

75 FR 35700 - Revisions to Forms, Statements, and Reporting Requirements for Natural Gas Pipelines

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-23

... filed in native applications or print-to-PDF format and not in a scanned format. Mail/Hand Delivery... also propose to revise page 520 accordingly. \\1\\ American Gas Association v. FERC, 593 F.3d 14 (D.C....\\14\\ \\14\\ 593 F.3d at 21. 8. Following the court's remand, AGA filed a motion requesting that the...

Cambio

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

Johnson, William

2015-10-19

Cambio opens data files from common gamma radiation detectors, displays a visual representation of it, and allows the user to edit the meta-data, as well as convert the data to a different file format.

Preliminary surficial geologic map database of the Amboy 30 x 60 minute quadrangle, California

USGS Publications Warehouse

Bedford, David R.; Miller, David M.; Phelps, Geoffrey A.

2006-01-01

The surficial geologic map database of the Amboy 30x60 minute quadrangle presents characteristics of surficial materials for an area approximately 5,000 km2 in the eastern Mojave Desert of California. This map consists of new surficial mapping conducted between 2000 and 2005, as well as compilations of previous surficial mapping. Surficial geology units are mapped and described based on depositional process and age categories that reflect the mode of deposition, pedogenic effects occurring post-deposition, and, where appropriate, the lithologic nature of the material. The physical properties recorded in the database focus on those that drive hydrologic, biologic, and physical processes such as particle size distribution (PSD) and bulk density. This version of the database is distributed with point data representing locations of samples for both laboratory determined physical properties and semi-quantitative field-based information. Future publications will include the field and laboratory data as well as maps of distributed physical properties across the landscape tied to physical process models where appropriate. The database is distributed in three parts: documentation, spatial map-based data, and printable map graphics of the database. Documentation includes this file, which provides a discussion of the surficial geology and describes the format and content of the map data, a database 'readme' file, which describes the database contents, and FGDC metadata for the spatial map information. Spatial data are distributed as Arc/Info coverage in ESRI interchange (e00) format, or as tabular data in the form of DBF3-file (.DBF) file formats. Map graphics files are distributed as Postscript and Adobe Portable Document Format (PDF) files, and are appropriate for representing a view of the spatial database at the mapped scale.

Rosetta: Ensuring the Preservation and Usability of ASCII-based Data into the Future

NASA Astrophysics Data System (ADS)

Ramamurthy, M. K.; Arms, S. C.

2015-12-01

Field data obtained from dataloggers often take the form of comma separated value (CSV) ASCII text files. While ASCII based data formats have positive aspects, such as the ease of accessing the data from disk and the wide variety of tools available for data analysis, there are some drawbacks, especially when viewing the situation through the lens of data interoperability and stewardship. The Unidata data translation tool, Rosetta, is a web-based service that provides an easy, wizard-based interface for data collectors to transform their datalogger generated ASCII output into Climate and Forecast (CF) compliant netCDF files following the CF-1.6 discrete sampling geometries. These files are complete with metadata describing what data are contained in the file, the instruments used to collect the data, and other critical information that otherwise may be lost in one of many README files. The choice of the machine readable netCDF data format and data model, coupled with the CF conventions, ensures long-term preservation and interoperability, and that future users will have enough information to responsibly use the data. However, with the understanding that the observational community appreciates the ease of use of ASCII files, methods for transforming the netCDF back into a CSV or spreadsheet format are also built-in. One benefit of translating ASCII data into a machine readable format that follows open community-driven standards is that they are instantly able to take advantage of data services provided by the many open-source data server tools, such as the THREDDS Data Server (TDS). While Rosetta is currently a stand-alone service, this talk will also highlight efforts to couple Rosetta with the TDS, thus allowing self-publishing of thoroughly documented datasets by the data producers themselves.

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

PubMed

Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

2011-01-01

Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

Data integration: Combined imaging and electrophysiology data in the cloud.

PubMed

Kini, Lohith G; Davis, Kathryn A; Wagenaar, Joost B

2016-01-01

There has been an increasing effort to correlate electrophysiology data with imaging in patients with refractory epilepsy over recent years. IEEG.org provides a free-access, rapidly growing archive of imaging data combined with electrophysiology data and patient metadata. It currently contains over 1200 human and animal datasets, with multiple data modalities associated with each dataset (neuroimaging, EEG, EKG, de-identified clinical and experimental data, etc.). The platform is developed around the concept that scientific data sharing requires a flexible platform that allows sharing of data from multiple file formats. IEEG.org provides high- and low-level access to the data in addition to providing an environment in which domain experts can find, visualize, and analyze data in an intuitive manner. Here, we present a summary of the current infrastructure of the platform, available datasets and goals for the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

Why mushrooms form gills: efficiency of the lamellate morphology

PubMed Central

FISCHER, Mark W. F.; MONEY, Nicholas P.

2009-01-01

Gilled mushrooms are produced by multiple orders within the Agaricomycetes. Some species form a single array of unbranched radial gills beneath their caps, many others produce multiple files of lamellulae between the primary gills, and branched gills are also common. In this largely theoretical study we modeled the effects of different gill arrangements on the total surface area for spore production. Relative to spore production over a flat surface, gills achieve a maximum 20-fold increase in surface area. The branching of gills produces the same increase in surface area as the formation of freestanding lamellulae (short gills). The addition of lamellulae between every second gill would offer a slightly greater increase in surface area in comparison to the addition of lamellulae between every pair of opposing gills, but this morphology does not appear in nature. Analysis of photographs of mushrooms demonstrates an excellent match between natural gill arrangements and configurations predicted by our model. PMID:20965062

Data integration: Combined Imaging and Electrophysiology data in the cloud

PubMed Central

Kini, Lohith G.; Davis, Kathryn A.; Wagenaar, Joost B.

2015-01-01

There has been an increasing effort to correlate electrophysiology data with imaging in patients with refractory epilepsy over recent years. IEEG.org provides a free-access, rapidly growing archive of imaging data combined with electrophysiology data and patient metadata. It currently contains over 1200 human and animal datasets, with multiple data modalities associated with each dataset (neuroimaging, EEG, EKG, de-identified clinical and experimental data, etc.). The platform is developed around the concept that scientific data sharing requires a flexible platform that allows sharing of data from multiple file-formats. IEEG.org provides high and low-level access to the data in addition to providing an environment in which domain experts can find, visualize, and analyze data in an intuitive manner. Here, we present a summary of the current infrastructure of the platform, available datasets and goals for the near future. PMID:26044858

The Jade File System. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Rao, Herman Chung-Hwa

1991-01-01

File systems have long been the most important and most widely used form of shared permanent storage. File systems in traditional time-sharing systems, such as Unix, support a coherent sharing model for multiple users. Distributed file systems implement this sharing model in local area networks. However, most distributed file systems fail to scale from local area networks to an internet. Four characteristics of scalability were recognized: size, wide area, autonomy, and heterogeneity. Owing to size and wide area, techniques such as broadcasting, central control, and central resources, which are widely adopted by local area network file systems, are not adequate for an internet file system. An internet file system must also support the notion of autonomy because an internet is made up by a collection of independent organizations. Finally, heterogeneity is the nature of an internet file system, not only because of its size, but also because of the autonomy of the organizations in an internet. The Jade File System, which provides a uniform way to name and access files in the internet environment, is presented. Jade is a logical system that integrates a heterogeneous collection of existing file systems, where heterogeneous means that the underlying file systems support different file access protocols. Because of autonomy, Jade is designed under the restriction that the underlying file systems may not be modified. In order to avoid the complexity of maintaining an internet-wide, global name space, Jade permits each user to define a private name space. In Jade's design, we pay careful attention to avoiding unnecessary network messages between clients and file servers in order to achieve acceptable performance. Jade's name space supports two novel features: (1) it allows multiple file systems to be mounted under one direction; and (2) it permits one logical name space to mount other logical name spaces. A prototype of Jade was implemented to examine and validate its design. The prototype consists of interfaces to the Unix File System, the Sun Network File System, and the File Transfer Protocol.

Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.

PubMed

Deelen, Patrick; Bonder, Marc Jan; van der Velde, K Joeri; Westra, Harm-Jan; Winder, Erwin; Hendriksen, Dennis; Franke, Lude; Swertz, Morris A

2014-12-11

To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about which genomic strand is used as reference. Genotype Harmonizer (GH) is a command-line tool to harmonize genetic datasets by automatically solving issues concerning genomic strand and file format. GH solves the unknown strand issue by aligning ambiguous A/T and G/C SNPs to a specified reference, using linkage disequilibrium patterns without prior knowledge of the used strands. GH supports many common GWAS/NGS genotype formats including PLINK, binary PLINK, VCF, SHAPEIT2 & Oxford GEN. GH is implemented in Java and a large part of the functionality can also be used as Java 'Genotype-IO' API. All software is open source under license LGPLv3 and available from http://www.molgenis.org/systemsgenetics. GH can be used to harmonize genetic datasets across different file formats and can be easily integrated as a step in routine meta-analysis and imputation pipelines.

BOREAS Elevation Contours over the NSA and SSA in ARC/INFO Generate Format

NASA Technical Reports Server (NTRS)

Knapp, David; Nickeson, Jaime; Hall, Forrest G. (Editor)

2000-01-01

This data set was prepared by BORIS Staff by reformatting the original data into the ARC/INFO Generate format. The original data were received in SIF at a scale of 1:50,000. BORIS staff could not find a format document or commercial software for reading SIF; the BOREAS HYD-08 team pro-vided some C source code that could read some of the SIF files. The data cover the BOREAS NSA and SSA. The original data were compiled from information available in the 1970s and 1980s. The data are available in ARC/INFO Generate format files.

Pre-Launch Algorithm and Data Format for the Level 1 Calibration Products for the EOS AM-1 Moderate Resolution Imaging Spectroradiometer (MODIS)

NASA Technical Reports Server (NTRS)

Guenther, Bruce W.; Godden, Gerald D.; Xiong, Xiao-Xiong; Knight, Edward J.; Qiu, Shi-Yue; Montgomery, Harry; Hopkins, M. M.; Khayat, Mohammad G.; Hao, Zhi-Dong; Smith, David E. (Technical Monitor)

2000-01-01

The Moderate Resolution Imaging Spectroradiometer (MODIS) radiometric calibration product is described for the thermal emissive and the reflective solar bands. Specific sensor design characteristics are identified to assist in understanding how the calibration algorithm software product is designed. The reflected solar band software products of radiance and reflectance factor both are described. The product file format is summarized and the MODIS Characterization Support Team (MCST) Homepage location for the current file format is provided.

Multiple autoclave cycle effects on cyclic fatigue of nickel-titanium rotary files produced by new manufacturing methods.

PubMed

Hilfer, Paul B; Bergeron, Brian E; Mayerchak, Michael J; Roberts, Howard W; Jeansonne, Billie G

2011-01-01

Novel nickel-titanium rotary files with proprietary manufacturing techniques have recently been marketed. The purpose of this study was to assess multiple autoclave cycle effects on cyclic fatigue of GT Series X files (Dentsply Tulsa Dental Specialties, Tulsa, OK) and Twisted Files (SybronEndo, Orange, CA) METHODS: A jig using a 5-mm radius curve with 90° of maximum file flexure was used to induce cyclic fatigue failure. Files (n = 10) representing each experimental group (GT Series X 20/.04 and 20/.06; Twisted Files 25/.04 and 25/.06) were first tested to establish baseline mean cycles to failure (MCF). Experimental groups (n = 20) were then cycled to 25% of the established baseline MCF and then autoclaved. Additional autoclaving was accomplished at 50% and 75% of MCF followed by continual testing until failure. Control groups (n = 20) underwent the same procedures except autoclaving was not accomplished. The GT Series X (20/.04 and 20/.06) files showed no significant difference (p = 0.918/p = 0.096) in MCF for experimental versus control files. Twisted Files (25/.04) showed no significant difference (p = 0.432) in MCF between experimental and control groups. However, the Twisted Files (25/.06) experimental group showed a significantly lower (p = 0.0175) MCF compared with the controls. Under the conditions of this evaluation, autoclave sterilization significantly decreased cyclic fatigue resistance of one of the four file groups tested. Repeated autoclaving significantly reduced the MCF of 25/.06 Twisted Files; however, 25/.04 Twisted Files and both GT Series X files tested were not significantly affected by the same conditions. Published by Elsevier Inc.

VizieR Online Data Catalog: Sgr B2(N) and Sgr B2(M) IRAM 30m line survey (Belloche+, 2013)

NASA Astrophysics Data System (ADS)

Belloche, A.; Mueller, H. S. P.; Menten, K. M.; Schilke, P.; Comito, C.

2013-08-01

The list of line identifications corresponding to the blue labels in Figs. 2 to 7 where the labels are often too crowded to be easily readable are available in ASCII format. The lists are split into six files, three for Sgr B2(N) and three for Sgr B2(M). For each source, there is one file per atmospheric window (3, 2, and 1mm). Each file is ordered by increasing frequency. The observed and synthetic spectra of Sgr B2(N) and Sgr B2(M) between 80 and 116GHz are available both in ASCII and FITS formats. The synthetic spectra were resampled to the same frequency channels as the observed spectra. The blanking value is -1000K for the ASCII files. There is one ASCII file per source. There are two FITS files per source, one for the observed spectrum and one for the synthetic spectrum. The intensities are in main-beam temperature scale in K. The blanking value is 42.75234K for the observed spectrum of SgrB2(N) and 53.96533K for the observed spectrum of SgrB2(M). (9 data files).

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

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

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

Use of Schema on Read in Earth Science Data Archives

NASA Technical Reports Server (NTRS)

Hegde, Mahabaleshwara; Smit, Christine; Pilone, Paul; Petrenko, Maksym; Pham, Long

2017-01-01

Traditionally, NASA Earth Science data archives have file-based storage using proprietary data file formats, such as HDF and HDF-EOS, which are optimized to support fast and efficient storage of spaceborne and model data as they are generated. The use of file-based storage essentially imposes an indexing strategy based on data dimensions. In most cases, NASA Earth Science data uses time as the primary index, leading to poor performance in accessing data in spatial dimensions. For example, producing a time series for a single spatial grid cell involves accessing a large number of data files. With exponential growth in data volume due to the ever-increasing spatial and temporal resolution of the data, using file-based archives poses significant performance and cost barriers to data discovery and access. Storing and disseminating data in proprietary data formats imposes an additional access barrier for users outside the mainstream research community. At the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), we have evaluated applying the schema-on-read principle to data access and distribution. We used Apache Parquet to store geospatial data, and have exposed data through Amazon Web Services (AWS) Athena, AWS Simple Storage Service (S3), and Apache Spark. Using the schema-on-read approach allows customization of indexing spatially or temporally to suit the data access pattern. The storage of data in open formats such as Apache Parquet has widespread support in popular programming languages. A wide range of solutions for handling big data lowers the access barrier for all users. This presentation will discuss formats used for data storage, frameworks with This presentation will discuss formats used for data storage, frameworks with support for schema-on-read used for data access, and common use cases covering data usage patterns seen in a geospatial data archive.

High-Throughput Tabular Data Processor - Platform independent graphical tool for processing large data sets.

PubMed

Madanecki, Piotr; Bałut, Magdalena; Buckley, Patrick G; Ochocka, J Renata; Bartoszewski, Rafał; Crossman, David K; Messiaen, Ludwine M; Piotrowski, Arkadiusz

2018-01-01

High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp).

High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets

PubMed Central

Bałut, Magdalena; Buckley, Patrick G.; Ochocka, J. Renata; Bartoszewski, Rafał; Crossman, David K.; Messiaen, Ludwine M.; Piotrowski, Arkadiusz

2018-01-01

High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp). PMID:29432475

A malware detection scheme based on mining format information.

PubMed

Bai, Jinrong; Wang, Junfeng; Zou, Guozhong

2014-01-01

Malware has become one of the most serious threats to computer information system and the current malware detection technology still has very significant limitations. In this paper, we proposed a malware detection approach by mining format information of PE (portable executable) files. Based on in-depth analysis of the static format information of the PE files, we extracted 197 features from format information of PE files and applied feature selection methods to reduce the dimensionality of the features and achieve acceptable high performance. When the selected features were trained using classification algorithms, the results of our experiments indicate that the accuracy of the top classification algorithm is 99.1% and the value of the AUC is 0.998. We designed three experiments to evaluate the performance of our detection scheme and the ability of detecting unknown and new malware. Although the experimental results of identifying new malware are not perfect, our method is still able to identify 97.6% of new malware with 1.3% false positive rates.

A Malware Detection Scheme Based on Mining Format Information

PubMed Central

Bai, Jinrong; Wang, Junfeng; Zou, Guozhong

2014-01-01

Malware has become one of the most serious threats to computer information system and the current malware detection technology still has very significant limitations. In this paper, we proposed a malware detection approach by mining format information of PE (portable executable) files. Based on in-depth analysis of the static format information of the PE files, we extracted 197 features from format information of PE files and applied feature selection methods to reduce the dimensionality of the features and achieve acceptable high performance. When the selected features were trained using classification algorithms, the results of our experiments indicate that the accuracy of the top classification algorithm is 99.1% and the value of the AUC is 0.998. We designed three experiments to evaluate the performance of our detection scheme and the ability of detecting unknown and new malware. Although the experimental results of identifying new malware are not perfect, our method is still able to identify 97.6% of new malware with 1.3% false positive rates. PMID:24991639

Revised Subsurface Stratigraphic Framework of the Fort Union and Wasatch Formations, Powder River Basin, Wyoming and Montana

USGS Publications Warehouse

Flores, Romeo M.; Spear, Brianne D.; Purchase, Peter A.; Gallagher, Craig M.

2010-01-01

Described in this report is an updated subsurface stratigraphic framework of the Paleocene Fort Union Formation and Eocene Wasatch Formation in the Powder River Basin (PRB) in Wyoming and Montana. This framework is graphically presented in 17 intersecting west-east and north-south cross sections across the basin. Also included are: (1) the dataset and all associated digital files and (2) digital files for all figures and table 1 suitable for large-format printing. The purpose of this U.S. Geological Survey (USGS) Open-File Report is to provide rapid dissemination and accessibility of the stratigraphic cross sections and related digital data to USGS customers, especially the U.S. Bureau of Land Management (BLM), to facilitate their modeling of the hydrostratigraphy of the PRB. This report contains a brief summary of the coal-bed correlations and database, and is part of a larger ongoing study that will be available in the near future.

Development of an e-VLBI Data Transport Software Suite with VDIF

NASA Technical Reports Server (NTRS)

Sekido, Mamoru; Takefuji, Kazuhiro; Kimura, Moritaka; Hobiger, Thomas; Kokado, Kensuke; Nozawa, Kentarou; Kurihara, Shinobu; Shinno, Takuya; Takahashi, Fujinobu

2010-01-01

We have developed a software library (KVTP-lib) for VLBI data transmission over the network with the VDIF (VLBI Data Interchange Format), which is the newly proposed standard VLBI data format designed for electronic data transfer over the network. The software package keeps the application layer (VDIF frame) and the transmission layer separate, so that each layer can be developed efficiently. The real-time VLBI data transmission tool sudp-send is an application tool based on the KVTP-lib library. sudp-send captures the VLBI data stream from the VSI-H interface with the K5/VSI PC-board and writes the data to file in standard Linux file format or transmits it to the network using the simple- UDP (SUDP) protocol. Another tool, sudp-recv , receives the data stream from the network and writes the data to file in a specific VLBI format (K5/VSSP, VDIF, or Mark 5B). This software system has been implemented on the Wettzell Tsukuba baseline; evaluation before operational employment is under way.

75 FR 19339 - FM Table of Allotments, Amboy, California

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-14

.... SUMMARY: The Audio Division seeks comments on a petition filed by Sunnylands Broadcasting, LLC, proposing... disabilities (Braille, large print, electronic files, audio format), send an e-mail to [email protected] or call... Chief, Audio Division, Media Bureau. [FR Doc. 2010-8449 Filed 4-13-10; 8:45 am] BILLING CODE 6712-01-S ...

14 CFR 221.121 - How to prepare and file applications for Special Tariff Permission.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., DEPARTMENT OF TRANSPORTATION (AVIATION PROCEEDINGS) ECONOMIC REGULATIONS TARIFFS Special Tariff Permission To... notice shall conform to the requirements of § 221.212 if filed electronically. (b) Number of paper copies and place of filing. For paper format applications, the original and one copy of each such application...

Biological Investigations of Adaptive Networks: Neuronal Control of Conditioned Responses

DTIC Science & Technology

1989-07-01

The program also controls A/D sampling of voltage trace from NMR transducer and disk files for NMR, neural spikes, and synchronization. * HSAD . Basic...format which ANALYZE (by John Desmond) can read. e FIG.HIRES Reads C-64 HSAD files and EVENT NMR files and generates oscilloscope-like figures showing

77 FR 6625 - Railroad Cost of Capital-2011

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-08

... railroads are due by May 9, 2012. ADDRESSES: Comments may be submitted either via the Board's e-filing system or in the traditional paper format. Any person using e-filing should comply with the instructions at the E-FILING link on the Board's Web site, at http://www.stb.dot.gov . Any person submitting a...

Students' Attitudes to and Usage of Academic Feedback Provided via Audio Files

ERIC Educational Resources Information Center

Merry, Stephen; Orsmond, Paul

2008-01-01

This study explores students' attitudes to the provision of formative feedback on academic work using audio files together with the ways in which students implement such feedback within their learning. Fifteen students received audio file feedback on written work and were subsequently interviewed regarding their utilisation of that feedback within…

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

PubMed

Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

2015-01-01

Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

New Powder Diffraction File (PDF-4) in relational database format: advantages and data-mining capabilities.

PubMed

Kabekkodu, Soorya N; Faber, John; Fawcett, Tim

2002-06-01

The International Centre for Diffraction Data (ICDD) is responding to the changing needs in powder diffraction and materials analysis by developing the Powder Diffraction File (PDF) in a very flexible relational database (RDB) format. The PDF now contains 136,895 powder diffraction patterns. In this paper, an attempt is made to give an overview of the PDF-4, search/match methods and the advantages of having the PDF-4 in RDB format. Some case studies have been carried out to search for crystallization trends, properties, frequencies of space groups and prototype structures. These studies give a good understanding of the basic structural aspects of classes of compounds present in the database. The present paper also reports data-mining techniques and demonstrates the power of a relational database over the traditional (flat-file) database structures.

Is HDF5 a Good Format to Replace UVFITS?

NASA Astrophysics Data System (ADS)

Price, D. C.; Barsdell, B. R.; Greenhill, L. J.

2015-09-01

The FITS (Flexible Image Transport System) data format was developed in the late 1970s for storage and exchange of astronomy-related image data. Since then, it has become a standard file format not only for images, but also for radio interferometer data (e.g. UVFITS, FITS-IDI). But is FITS the right format for next-generation telescopes to adopt? The newer Hierarchical Data Format (HDF5) file format offers considerable advantages over FITS, but has yet to gain widespread adoption within the radio astronomy. One of the major holdbacks is that HDF5 is not well supported by data reduction software packages. Here, we present a comparison of FITS, HDF5, and the MeasurementSet (MS) format for storage of interferometric data. In addition, we present a tool for converting between formats. We show that the underlying data model of FITS can be ported to HDF5, a first step toward achieving wider HDF5 support.

49 CFR 360.3 - Filing fees.

Code of Federal Regulations, 2010 CFR

2010-10-01

... INSURANCE § 360.3 Filing fees. (a) Manner of payment. (1) Except for the insurance fees described in the... withdrawn. (d) Related or consolidated proceedings. (1) Separate fees need not be paid for related... requests for multiple types of operating authority filed on forms in the OP-1 series under the regulations...

49 CFR 360.3 - Filing fees.

Code of Federal Regulations, 2013 CFR

2013-10-01

... INSURANCE § 360.3 Filing fees. (a) Manner of payment. (1) Except for the insurance fees described in the... withdrawn. (d) Related or consolidated proceedings. (1) Separate fees need not be paid for related... requests for multiple types of operating authority filed on forms in the OP-1 series under the regulations...

49 CFR 360.3 - Filing fees.

Code of Federal Regulations, 2011 CFR

2011-10-01

... INSURANCE § 360.3 Filing fees. (a) Manner of payment. (1) Except for the insurance fees described in the... withdrawn. (d) Related or consolidated proceedings. (1) Separate fees need not be paid for related... requests for multiple types of operating authority filed on forms in the OP-1 series under the regulations...

49 CFR 360.3 - Filing fees.

Code of Federal Regulations, 2012 CFR

2012-10-01

... INSURANCE § 360.3 Filing fees. (a) Manner of payment. (1) Except for the insurance fees described in the... withdrawn. (d) Related or consolidated proceedings. (1) Separate fees need not be paid for related... requests for multiple types of operating authority filed on forms in the OP-1 series under the regulations...

BOREAS TE-20 Soils Data Over the NSA-MSA and Tower Sites in Raster Format

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Veldhuis, Hugo; Knapp, David; Veldhuis, Hugo

2000-01-01

The BOREAS TE-20 team collected several data sets for use in developing and testing models of forest ecosystem dynamics. This data set was gridded from vector layers of soil maps that were received from Dr. Hugo Veldhuis, who did the original mapping in the field during 1994. The vector layers were gridded into raster files that cover the NSA-MSA and tower sites. The data are stored in binary, image format files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Center (DAAC).

Covariance Data File Formats for Whisper-1.0 & Whisper-1.1

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

Brown, Forrest B.; Rising, Michael Evan

2017-01-09

Whisper is a statistical analysis package developed in 2014 to support nuclear criticality safety (NCS) validation. It uses the sensitivity profile data for an application as computed by MCNP6 along with covariance files for the nuclear data to determine a baseline upper-subcritical-limit (USL) for the application. Whisper version 1.0 was first developed and used at LANL in 2014. During 2015-2016, Whisper was updated to version 1.1 and is to be included with the upcoming release of MCNP6.2. This report describes the file formats used for the covariance data in both Whisper-1.0 and Whisper-1.1.

Tool for Merging Proposals Into DSN Schedules

NASA Technical Reports Server (NTRS)

Khanampornpan, Teerapat; Kwok, John; Call, Jared

2008-01-01

A Practical Extraction and Reporting Language (Perl) script called merge7da has been developed to facilitate determination, by a project scheduler in NASA's Deep Space Network, of whether a proposal for use of the DSN could create a conflict with the current DSN schedule. Prior to the development of merge7da, there was no way to quickly identify potential schedule conflicts: it was necessary to submit a proposal and wait a day or two for a response from a DSN scheduling facility. By using merge7da to detect and eliminate potential schedule conflicts before submitting a proposal, a project scheduler saves time and gains assurance that the proposal will probably be accepted. merge7da accepts two input files, one of which contains the current DSN schedule and is in a DSN-standard format called '7da'. The other input file contains the proposal and is in another DSN-standard format called 'C1/C2'. merge7da processes the two input files to produce a merged 7da-format output file that represents the DSN schedule as it would be if the proposal were to be adopted. This 7da output file can be loaded into various DSN scheduling software tools now in use.

Effectiveness of source documents for identifying fatal occupational injuries: a synthesis of studies.

PubMed

Stout, N; Bell, C

1991-06-01

The complete and accurate identification of fatal occupational injuries among the US work force is an important first step in developing work injury prevention efforts. Numerous sources of information, such as death certificates, Workers' Compensation files, Occupational Safety and Health Administration (OSHA) files, medical examiner records, state health and labor department reports, and various combinations of these, have been used to identify cases of work-related fatal injuries. Recent studies have questioned the effectiveness of these sources for identifying such cases. At least 10 studies have used multiple sources to define the universe of fatal work injuries within a state and to determine the capture rates, or proportion of the universe identified, by each source. Results of these studies, which are not all available in published literature, are summarized here in a format that allows researchers to readily compare the ascertainment capabilities of the sources. The overall average capture rates of sources were as follows: death certificates, 81%; medical examiner records, 61%; Workers' Compensation reports, 57%; and OSHA reports 32%. Variations by state and value added through the use of multiple sources are presented and discussed. This meta-analysis of 10 state-based studies summarizes the effectiveness of various source documents for capturing cases of fatal occupational injuries to help researchers make informed decisions when designing occupational injury surveillance systems.

Effectiveness of source documents for identifying fatal occupational injuries: a synthesis of studies.

PubMed Central

Stout, N; Bell, C

1991-01-01

BACKGROUND: The complete and accurate identification of fatal occupational injuries among the US work force is an important first step in developing work injury prevention efforts. Numerous sources of information, such as death certificates, Workers' Compensation files, Occupational Safety and Health Administration (OSHA) files, medical examiner records, state health and labor department reports, and various combinations of these, have been used to identify cases of work-related fatal injuries. Recent studies have questioned the effectiveness of these sources for identifying such cases. METHODS: At least 10 studies have used multiple sources to define the universe of fatal work injuries within a state and to determine the capture rates, or proportion of the universe identified, by each source. Results of these studies, which are not all available in published literature, are summarized here in a format that allows researchers to readily compare the ascertainment capabilities of the sources. RESULTS: The overall average capture rates of sources were as follows: death certificates, 81%; medical examiner records, 61%; Workers' Compensation reports, 57%; and OSHA reports 32%. Variations by state and value added through the use of multiple sources are presented and discussed. CONCLUSIONS: This meta-analysis of 10 state-based studies summarizes the effectiveness of various source documents for capturing cases of fatal occupational injuries to help researchers make informed decisions when designing occupational injury surveillance systems. PMID:1827569

78 FR 6173 - Diana Del Grosso, Ray Smith, Joseph Hatch, Cheryl Hatch, Kathleen Kelley, Andrew Wilklund, and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-29

... submissions by the parties may be submitted via the Board's e-filing format or in the traditional paper format. Any person using e-filing should attach a document and otherwise comply with the instructions at the E... proceeding under 49 U.S.C. 721 and 5 U.S.C. 554(e). Petitioners request that the Board declare that specific...

Occupational Survey Report. Visual Information, AFSC 3V0X1

DTIC Science & Technology

2000-04-01

of the career ladder include: Scan artwork using flatbed scanners Convert graphic file formats Design layouts Letter certificates using laser...Design layouts Scan artwork using flatbed scanners Produce artwork using mouse or digitizing tablets Design and produce imagery for web pages Produce...DAFSC 3V031 PERSONNEL TASKS A0034 Scan artwork using flatbed scanners C0065 Design layouts A0004 Convert graphic file formats A0006 Create

Transforming Dermatologic Imaging for the Digital Era: Metadata and Standards.

PubMed

Caffery, Liam J; Clunie, David; Curiel-Lewandrowski, Clara; Malvehy, Josep; Soyer, H Peter; Halpern, Allan C

2018-01-17

Imaging is increasingly being used in dermatology for documentation, diagnosis, and management of cutaneous disease. The lack of standards for dermatologic imaging is an impediment to clinical uptake. Standardization can occur in image acquisition, terminology, interoperability, and metadata. This paper presents the International Skin Imaging Collaboration position on standardization of metadata for dermatologic imaging. Metadata is essential to ensure that dermatologic images are properly managed and interpreted. There are two standards-based approaches to recording and storing metadata in dermatologic imaging. The first uses standard consumer image file formats, and the second is the file format and metadata model developed for the Digital Imaging and Communication in Medicine (DICOM) standard. DICOM would appear to provide an advantage over using consumer image file formats for metadata as it includes all the patient, study, and technical metadata necessary to use images clinically. Whereas, consumer image file formats only include technical metadata and need to be used in conjunction with another actor-for example, an electronic medical record-to supply the patient and study metadata. The use of DICOM may have some ancillary benefits in dermatologic imaging including leveraging DICOM network and workflow services, interoperability of images and metadata, leveraging existing enterprise imaging infrastructure, greater patient safety, and better compliance to legislative requirements for image retention.

Increasing the availability and usability of terrestrial ecology data through geospatial Web services and visualization tools (Invited)

NASA Astrophysics Data System (ADS)

Santhana Vannan, S.; Cook, R. B.; Wilson, B. E.; Wei, Y.

2010-12-01

Terrestrial ecology data sets are produced from diverse data sources such as model output, field data collection, laboratory analysis and remote sensing observation. These data sets can be created, distributed, and consumed in diverse ways as well. However, this diversity can hinder the usability of the data, and limit data users’ abilities to validate and reuse data for science and application purposes. Geospatial web services, such as those described in this paper, are an important means of reducing this burden. Terrestrial ecology researchers generally create the data sets in diverse file formats, with file and data structures tailored to the specific needs of their project, possibly as tabular data, geospatial images, or documentation in a report. Data centers may reformat the data to an archive-stable format and distribute the data sets through one or more protocols, such as FTP, email, and WWW. Because of the diverse data preparation, delivery, and usage patterns, users have to invest time and resources to bring the data into the format and structure most useful for their analysis. This time-consuming data preparation process shifts valuable resources from data analysis to data assembly. To address these issues, the ORNL DAAC, a NASA-sponsored terrestrial ecology data center, has utilized geospatial Web service technology, such as Open Geospatial Consortium (OGC) Web Map Service (WMS) and OGC Web Coverage Service (WCS) standards, to increase the usability and availability of terrestrial ecology data sets. Data sets are standardized into non-proprietary file formats and distributed through OGC Web Service standards. OGC Web services allow the ORNL DAAC to store data sets in a single format and distribute them in multiple ways and formats. Registering the OGC Web services through search catalogues and other spatial data tools allows for publicizing the data sets and makes them more available across the Internet. The ORNL DAAC has also created a Web-based graphical user interface called Spatial Data Access Tool (SDAT) that utilizes OGC Web services standards and allows data distribution and consumption for users not familiar with OGC standards. SDAT also allows for users to visualize the data set prior to download. Google Earth visualizations of the data set are also provided through SDAT. The use of OGC Web service standards at the ORNL DAAC has enabled an increase in data consumption. In one case, a data set had ~10 fold increase in download through OGC Web service in comparison to the conventional FTP and WWW method of access. The increase in download suggests that users are not only finding the data sets they need but also able to consume them readily in the format they need.

Toolsets for Airborne Data (TAD): Improving Machine Readability for ICARTT Data Files

NASA Astrophysics Data System (ADS)

Northup, E. A.; Early, A. B.; Beach, A. L., III; Kusterer, J.; Quam, B.; Wang, D.; Chen, G.

2015-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The ASDC Toolsets for Airborne Data (TAD) is designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. TAD makes use of aircraft data stored in the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) file format. ICARTT has been the NASA standard since 2010, and is widely used by NOAA, NSF, and international partners (DLR, FAAM). Its level of acceptance is due in part to it being generally self-describing for researchers, i.e., it provides necessary data descriptions for proper research use. Despite this, there are a number of issues with the current ICARTT format, especially concerning the machine readability. In order to overcome these issues, the TAD team has developed an "idealized" file format. This format is ASCII and is sufficiently machine readable to sustain the TAD system, however, it is not fully compatible with the current ICARTT format. The process of mapping ICARTT metadata to the idealized format, the format specifics, and the actual conversion process will be discussed. The goal of this presentation is to demonstrate an example of how to improve the machine readability of ASCII data format protocols.

SW New Mexico Oil Well Formation Tops

DOE Data Explorer

Shari Kelley

2015-10-21

Rock formation top picks from oil wells from southwestern New Mexico from scout cards and other sources. There are differing formation tops interpretations for some wells, so for those wells duplicate formation top data are presented in this file.

Methods and apparatus for capture and storage of semantic information with sub-files in a parallel computing system

DOEpatents

Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Torres, Aaron

2015-02-03

Techniques are provided for storing files in a parallel computing system using sub-files with semantically meaningful boundaries. A method is provided for storing at least one file generated by a distributed application in a parallel computing system. The file comprises one or more of a complete file and a plurality of sub-files. The method comprises the steps of obtaining a user specification of semantic information related to the file; providing the semantic information as a data structure description to a data formatting library write function; and storing the semantic information related to the file with one or more of the sub-files in one or more storage nodes of the parallel computing system. The semantic information provides a description of data in the file. The sub-files can be replicated based on semantically meaningful boundaries.

COVART 6.1: FASTGEN Legacy Model User’s Manual

DTIC Science & Technology

2010-03-31

Program Office • Crystal Gateway #4 • Suite 1103 • 200 12 th St. South • Arlington, VA 22202 REPORT DOCUMENTATION PAGE Form Approved... Single Proximity Burst File Layout ................................................ 208 Figure 23-2 OFRAGB Multiple Proximity Burst File Layout...dimensional normal, distribution of shotlines about an aim point (SHOT1) 2. Multiple shotlines over a two-dimensional grid (SHOT2) 3. A single shotline at

Multiple Independent File Parallel I/O with HDF5

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

Miller, M. C.

2016-07-13

The HDF5 library has supported the I/O requirements of HPC codes at Lawrence Livermore National Labs (LLNL) since the late 90’s. In particular, HDF5 used in the Multiple Independent File (MIF) parallel I/O paradigm has supported LLNL code’s scalable I/O requirements and has recently been gainfully used at scales as large as O(10 6) parallel tasks.

Standard interface files and procedures for reactor physics codes, version III

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

Carmichael, B.M.

Standards and procedures for promoting the exchange of reactor physics codes are updated to Version-III status. Standards covering program structure, interface files, file handling subroutines, and card input format are included. The implementation status of the standards in codes and the extension of the standards to new code areas are summarized. (15 references) (auth)

75 FR 19338 - FM TABLE OF ALLOTMENTS, Milford, Utah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-14

.... SUMMARY: The Audio Division seeks comments on a petition filed by Canyon Media Group, LLC, authorized..., large print, electronic files, audio format), send an e-mail to [email protected] or call the Consumer... Chief, Audio Division, Media Bureau. [FR Doc. 2010-8448 Filed 4-13-10; 8:45 am] BILLING CODE 6712-01-S ...

Snake River Plain Geothermal Play Fairway Analysis - Phase 1 KMZ files

DOE Data Explorer

John Shervais

2015-10-10

This dataset contain raw data files in kmz files (Google Earth georeference format). These files include volcanic vent locations and age, the distribution of fine-grained lacustrine sediments (which act as both a seal and an insulating layer for hydrothermal fluids), and post-Miocene faults compiled from the Idaho Geological Survey, the USGS Quaternary Fault database, and unpublished mapping. It also contains the Composite Common Risk Segment Map created during Phase 1 studies, as well as a file with locations of select deep wells used to interrogate the subsurface.

Plan for DoD Wide Demonstrations of a DoD Improved Interactive Electronic Technical Manual (IETM) Architecture

DTIC Science & Technology

1998-07-01

all the MS Word files into FrameMaker + SGML format and use the FrameMaker application to SGML tag all of the data in accordance with the Army TM...Document Type Definitions (DTDs) in MIL-STD- 2361. The edited SGML tagged files are saved as PDF files for delivery to the field. The FrameMaker ...as TIFF files and being imported into FrameMaker prior to saving the TMs as PDF files. Since the hardware to be used by the AN/PPS-5 technician is

Cytoscape file of chemical networks

EPA Pesticide Factsheets

The maximum connectivity scores of pairwise chemical conditions summarized from Cmap results in a file with Cytoscape format (http://www.cytoscape.org/). The figures in the publication were generated from this file. The Cytoscape file is formed from importing the eight text file therein.This dataset is associated with the following publication:Wang , R., A. Biales , N. Garcia-Reyero, E. Perkins, D. Villeneuve, G. Ankley, and D. Bencic. Fish Connectivity Mapping: Linking Chemical Stressors by Their MOA-Driven Transcriptomic Profiles. BMC Genomics. BioMed Central Ltd, London, UK, 17(84): 1-20, (2016).

FEAT - FAILURE ENVIRONMENT ANALYSIS TOOL (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Pack, G.

1994-01-01

The Failure Environment Analysis Tool, FEAT, enables people to see and better understand the effects of failures in a system. FEAT uses digraph models to determine what will happen to a system if a set of failure events occurs and to identify the possible causes of a selected set of failures. Failures can be user-selected from either engineering schematic or digraph model graphics, and the effects or potential causes of the failures will be color highlighted on the same schematic or model graphic. As a design tool, FEAT helps design reviewers understand exactly what redundancies have been built into a system and where weaknesses need to be protected or designed out. A properly developed digraph will reflect how a system functionally degrades as failures accumulate. FEAT is also useful in operations, where it can help identify causes of failures after they occur. Finally, FEAT is valuable both in conceptual development and as a training aid, since digraphs can identify weaknesses in scenarios as well as hardware. Digraphs models for use with FEAT are generally built with the Digraph Editor, a Macintosh-based application which is distributed with FEAT. The Digraph Editor was developed specifically with the needs of FEAT users in mind and offers several time-saving features. It includes an icon toolbox of components required in a digraph model and a menu of functions for manipulating these components. It also offers FEAT users a convenient way to attach a formatted textual description to each digraph node. FEAT needs these node descriptions in order to recognize nodes and propagate failures within the digraph. FEAT users store their node descriptions in modelling tables using any word processing or spreadsheet package capable of saving data to an ASCII text file. From within the Digraph Editor they can then interactively attach a properly formatted textual description to each node in a digraph. Once descriptions are attached to them, a selected set of nodes can be saved as a library file which represents a generic digraph structure for a class of components. The Generate Model feature can then use library files to generate digraphs for every component listed in the modeling tables, and these individual digraph files can be used in a variety of ways to speed generation of complete digraph models. FEAT contains a preprocessor which performs transitive closure on the digraph. This multi-step algorithm builds a series of phantom bridges, or gates, that allow accurate bi-directional processing of digraphs. This preprocessing can be time-consuming, but once preprocessing is complete, queries can be answered and displayed within seconds. A UNIX X-Windows port of version 3.5 of FEAT, XFEAT, is also available to speed the processing of digraph models created on the Macintosh. FEAT v3.6, which is only available for the Macintosh, has some report generation capabilities which are not available in XFEAT. For very large integrated systems, FEAT can be a real cost saver in terms of design evaluation, training, and knowledge capture. The capability of loading multiple digraphs and schematics into FEAT allows modelers to build smaller, more focused digraphs. Typically, each digraph file will represent only a portion of a larger failure scenario. FEAT will combine these files and digraphs from other modelers to form a continuous mathematical model of the system's failure logic. Since multiple digraphs can be cumbersome to use, FEAT ties propagation results to schematic drawings produced using MacDraw II (v1.1v2 or later) or MacDraw Pro. This makes it easier to identify single and double point failures that may have to cross several system boundaries and multiple engineering disciplines before creating a hazardous condition. FEAT v3.6 for the Macintosh is written in C-language using Macintosh Programmer's Workshop C v3.2. It requires at least a Mac II series computer running System 7 or System 6.0.8 and 32 Bit QuickDraw. It also requires a math coprocessor or coprocessor emulator and a color monitor (or one with 256 gray scale capability). A minimum of 4Mb of free RAM is highly recommended. The UNIX version of FEAT includes both FEAT v3.6 for the Macintosh and XFEAT. XFEAT is written in C-language for Sun series workstations running SunOS, SGI workstations running IRIX, DECstations running ULTRIX, and Intergraph workstations running CLIX version 6. It requires the MIT X Window System, Version 11 Revision 4, with OSF/Motif 1.1.3, and 16Mb of RAM. The standard distribution medium for FEAT 3.6 (Macintosh version) is a set of three 3.5 inch Macintosh format diskettes. The standard distribution package for the UNIX version includes the three FEAT 3.6 Macintosh diskettes plus a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format which contains XFEAT. Alternate distribution media and formats for XFEAT are available upon request. FEAT has been under development since 1990. Both FEAT v3.6 for the Macintosh and XFEAT v3.5 were released in 1993.

Index files for Belle II - very small skim containers

NASA Astrophysics Data System (ADS)

Sevior, Martin; Bloomfield, Tristan; Kuhr, Thomas; Ueda, I.; Miyake, H.; Hara, T.

2017-10-01

The Belle II experiment[1] employs the root file format[2] for recording data and is investigating the use of “index-files” to reduce the size of data skims. These files contain pointers to the location of interesting events within the total Belle II data set and reduce the size of data skims by 2 orders of magnitude. We implement this scheme on the Belle II grid by recording the parent file metadata and the event location within the parent file. While the scheme works, it is substantially slower than a normal sequential read of standard skim files using default root file parameters. We investigate the performance of the scheme by adjusting the “splitLevel” and “autoflushsize” parameters of the root files in the parent data files.

Improving medical records filing in a municipal hospital in Ghana.

PubMed

Teviu, E A A; Aikins, M; Abdulai, T I; Sackey, S; Boni, P; Afari, E; Wurapa, F

2012-09-01

Medical records are kept in the interest of both the patient and clinician. Proper filing of patient's medical records ensures easy retrieval and contributes to decreased patient waiting time at the hospital and continuity of care. This paper reports on an intervention study to address the issue of misfiling and multiple patient folders in a health facility. Intervention study. Municipal Hospital, Goaso, Asunafo North District, Brong Ahafo Region, Ghana. Methods employed for data collection were records review, direct observation and tracking of folders. Interventions instituted were staff durbars, advocacy and communication, consultations, in-service trainings, procurement and monitoring. Factors contributing to issuance of multiple folders and misfiling were determined. Proportion of multiple folders was estimated. Results revealed direct and indirect factors contributing to issuance of multiple patient folders and misfiling. Interventions and monitoring reduce acquisition of numerous medical folders per patient and misfiling. After the intervention, there was significant reduction in the use of multiple folders (i.e., overall 97% reduction) and a high usage of single patient medical folders (i.e., 99%). In conclusion, a defined medical records filing system with adequate training, logistics and regular monitoring and supervision minimises issuance of multiple folders and misfiling.

18 CFR 270.304 - Tight formation gas.

Code of Federal Regulations, 2011 CFR

2011-04-01

... determination that natural gas is tight formation gas must file with the jurisdictional agency an application... formation; (d) A complete copy of the well log, including the log heading identifying the designated tight...

Proposal for a Standard Format for Neurophysiology Data Recording and Exchange.

PubMed

Stead, Matt; Halford, Jonathan J

2016-10-01

The lack of interoperability between information networks is a significant source of cost in health care. Standardized data formats decrease health care cost, improve quality of care, and facilitate biomedical research. There is no common standard digital format for storing clinical neurophysiologic data. This review proposes a new standard file format for neurophysiology data (the bulk of which is video-electroencephalographic data), entitled the Multiscale Electrophysiology Format, version 3 (MEF3), which is designed to address many of the shortcomings of existing formats. MEF3 provides functionality that addresses many of the limitations of current formats. The proposed improvements include (1) hierarchical file structure with improved organization; (2) greater extensibility for big data applications requiring a large number of channels, signal types, and parallel processing; (3) efficient and flexible lossy or lossless data compression; (4) industry standard multilayered data encryption and time obfuscation that permits sharing of human data without the need for deidentification procedures; (5) resistance to file corruption; (6) facilitation of online and offline review and analysis; and (7) provision of full open source documentation. At this time, there is no other neurophysiology format that supports all of these features. MEF3 is currently gaining industry and academic community support. The authors propose the use of the MEF3 as a standard format for neurophysiology recording and data exchange. Collaboration between industry, professional organizations, research communities, and independent standards organizations is needed to move the project forward.

HDFITS: Porting the FITS data model to HDF5

NASA Astrophysics Data System (ADS)

Price, D. C.; Barsdell, B. R.; Greenhill, L. J.

2015-09-01

The FITS (Flexible Image Transport System) data format has been the de facto data format for astronomy-related data products since its inception in the late 1970s. While the FITS file format is widely supported, it lacks many of the features of more modern data serialization, such as the Hierarchical Data Format (HDF5). The HDF5 file format offers considerable advantages over FITS, such as improved I/O speed and compression, but has yet to gain widespread adoption within astronomy. One of the major holdbacks is that HDF5 is not well supported by data reduction software packages and image viewers. Here, we present a comparison of FITS and HDF5 as a format for storage of astronomy datasets. We show that the underlying data model of FITS can be ported to HDF5 in a straightforward manner, and that by doing so the advantages of the HDF5 file format can be leveraged immediately. In addition, we present a software tool, fits2hdf, for converting between FITS and a new 'HDFITS' format, where data are stored in HDF5 in a FITS-like manner. We show that HDFITS allows faster reading of data (up to 100x of FITS in some use cases), and improved compression (higher compression ratios and higher throughput). Finally, we show that by only changing the import lines in Python-based FITS utilities, HDFITS formatted data can be presented transparently as an in-memory FITS equivalent.

What is meant by Format Version? Product Version? Collection?

Atmospheric Science Data Center

2017-10-12

The format Version is used to distinguish between software deliveries to ASDC that result in a product format change. The format version is given in the MISR data file name using the designator _Fnn_ where nn is the version number. ...

ListingAnalyst: A program for analyzing the main output file from MODFLOW

USGS Publications Warehouse

Winston, Richard B.; Paulinski, Scott

2014-01-01

ListingAnalyst is a Windows® program for viewing the main output file from MODFLOW-2005, MODFLOW-NWT, or MODFLOW-LGR. It organizes and displays large files quickly without using excessive memory. The sections and subsections of the file are displayed in a tree-view control, which allows the user to navigate quickly to desired locations in the files. ListingAnalyst gathers error and warning messages scattered throughout the main output file and displays them all together in an error and a warning tab. A grid view displays tables in a readable format and allows the user to copy the table into a spreadsheet. The user can also search the file for terms of interest.

Recent enhancements to the GRIDGEN structured grid generation system

NASA Technical Reports Server (NTRS)

Steinbrenner, John P.; Chawner, John R.

1992-01-01

Significant enhancements are being implemented into the GRIDGEN3D, multiple block, structured grid generation software. Automatic, point-to-point, interblock connectivity will be possible through the addition of the domain entity to GRIDBLOCK's block construction process. Also, the unification of GRIDGEN2D and GRIDBLOCK has begun with the addition of edge grid point distribution capability to GRIDBLOCK. The geometric accuracy of surface grids and the ease with which databases may be obtained is being improved by adding support for standard computer-aided design formats (e.g., PATRAN Neutral and IGES files). Finally, volume grid quality was improved through addition of new SOR algorithm features and the new hybrid control function type to GRIDGEN3D.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

Vector Topographic Map Data over the BOREAS NSA and SSA in SIF Format

NASA Technical Reports Server (NTRS)

Knapp, David; Nickeson, Jaime; Hall, Forrest G. (Editor)

2000-01-01

This data set contains vector contours and other features of individual topographic map sheets from the National Topographic Series (NTS). The map sheet files were received in Standard Interchange Format (SIF) and cover the BOReal Ecosystem-Atmosphere Study (BOREAS) Northern Study Area (NSA) and Southern Study Area (SSA) at scales of 1:50,000 and 1:250,000. The individual files are stored in compressed Unix tar archives.

Workflow opportunities using JPEG 2000

NASA Astrophysics Data System (ADS)

Foshee, Scott

2002-11-01

JPEG 2000 is a new image compression standard from ISO/IEC JTC1 SC29 WG1, the Joint Photographic Experts Group (JPEG) committee. Better thought of as a sibling to JPEG rather than descendant, the JPEG 2000 standard offers wavelet based compression as well as companion file formats and related standardized technology. This paper examines the JPEG 2000 standard for features in four specific areas-compression, file formats, client-server, and conformance/compliance that enable image workflows.

GIF Animation of Mode Shapes and Other Data on the Internet

NASA Technical Reports Server (NTRS)

Pappa, Richard S.

1998-01-01

The World Wide Web abounds with animated cartoons and advertisements competing for our attention. Most of these figures are animated Graphics Interchange Format (GIF) files. These files contain a series of ordinary GIF images plus control information, and they provide an exceptionally simple, effective way to animate on the Internet. To date, however, this format has rarely been used for technical data, although there is no inherent reason not to do so. This paper describes a procedure for creating high-resolution animated GIFs of mode shapes and other types of structural dynamics data with readily available software. The paper shows three example applications using recent modal test data and video footage of a high-speed sled run. A fairly detailed summary of the GIF file format is provided in the appendix. All of the animations discussed in the paper are posted on the Internet available through the following address: http://sdb-www.larc.nasa.gov/.

Preparing PNNL Reports with LaTeX

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

Waichler, Scott R.

2005-06-01

LaTeX is a mature document preparation system that is the standard in many scientific and academic workplaces. It has been used extensively by scattered individuals and research groups within PNNL for years, but until now there have been no centralized or lab-focused resources to help authors and editors. PNNL authors and editors can produce correctly formatted PNNL or PNWD reports using the LaTeX document preparation system and the available template files. Please visit the PNNL-LaTeX Project (http://stidev.pnl.gov/resources/latex/, inside the PNNL firewall) for additional information and files. In LaTeX, document content is maintained separately from document structure for the most part.more » This means that the author can easily produce the same content in different formats and, more importantly, can focus on the content and write it in a plain text file that doesn't go awry, is easily transferable, and won't become obsolete due to software changes. LaTeX produces the finest print quality output; its typesetting is noticeably better than that of MS Word. This is particularly true for mathematics, tables, and other types of special text. Other benefits of LaTeX: easy handling of large numbers of figures and tables; automatic and error-free captioning, citation, cross-referencing, hyperlinking, and indexing; excellent published and online documentation; free or low-cost distributions for Windows/Linux/Unix/Mac OS X. This document serves two purposes: (1) it provides instructions to produce reports formatted to PNNL requirements using LaTeX, and (2) the document itself is in the form of a PNNL report, providing examples of many solved formatting challenges. Authors can use this document or its skeleton version (with formatting examples removed) as the starting point for their own reports. The pnnreport.cls class file and pnnl.bst bibliography style file contain the required formatting specifications for reports to the Department of Energy. Options are also provided for formatting PNWD (non-1830) reports. This documentation and the referenced files are meant to provide a complete package of PNNL particulars for authors and editors who wish to prepare technical reports using LaTeX. The example material in this document was borrowed from real reports and edited for demonstration purposes. The subject matter content of the example material is not relevant here and generally does not make literal sense in the context of this document. Brackets ''[]'' are used to denote large blocks of example text. The PDF file for this report contains hyperlinks to facilitate navigation. Hyperlinks are provided for all cross-referenced material, including section headings, figures, tables, and references. Not all hyperlinks are colored but will be obvious when you move your mouse over them.« less

Publications - PIR 2002-3 | Alaska Division of Geological & Geophysical

Science.gov Websites

): Philip Smith Mountains Bibliographic Reference Stevens, D.S.P., 2014, Engineering-geologic map of the Digital Geospatial Data Philip Smith Mountains: Engineering-geologic map Data File Format File Size Info

Scalable Earth-observation Analytics for Geoscientists: Spacetime Extensions to the Array Database SciDB

NASA Astrophysics Data System (ADS)

Appel, Marius; Lahn, Florian; Pebesma, Edzer; Buytaert, Wouter; Moulds, Simon

2016-04-01

Today's amount of freely available data requires scientists to spend large parts of their work on data management. This is especially true in environmental sciences when working with large remote sensing datasets, such as obtained from earth-observation satellites like the Sentinel fleet. Many frameworks like SpatialHadoop or Apache Spark address the scalability but target programmers rather than data analysts, and are not dedicated to imagery or array data. In this work, we use the open-source data management and analytics system SciDB to bring large earth-observation datasets closer to analysts. Its underlying data representation as multidimensional arrays fits naturally to earth-observation datasets, distributes storage and computational load over multiple instances by multidimensional chunking, and also enables efficient time-series based analyses, which is usually difficult using file- or tile-based approaches. Existing interfaces to R and Python furthermore allow for scalable analytics with relatively little learning effort. However, interfacing SciDB and file-based earth-observation datasets that come as tiled temporal snapshots requires a lot of manual bookkeeping during ingestion, and SciDB natively only supports loading data from CSV-like and custom binary formatted files, which currently limits its practical use in earth-observation analytics. To make it easier to work with large multi-temporal datasets in SciDB, we developed software tools that enrich SciDB with earth observation metadata and allow working with commonly used file formats: (i) the SciDB extension library scidb4geo simplifies working with spatiotemporal arrays by adding relevant metadata to the database and (ii) the Geospatial Data Abstraction Library (GDAL) driver implementation scidb4gdal allows to ingest and export remote sensing imagery from and to a large number of file formats. Using added metadata on temporal resolution and coverage, the GDAL driver supports time-based ingestion of imagery to existing multi-temporal SciDB arrays. While our SciDB plugin works directly in the database, the GDAL driver has been specifically developed using a minimum amount of external dependencies (i.e. CURL). Source code for both tools is available from github [1]. We present these tools in a case-study that demonstrates the ingestion of multi-temporal tiled earth-observation data to SciDB, followed by a time-series analysis using R and SciDBR. Through the exclusive use of open-source software, our approach supports reproducibility in scalable large-scale earth-observation analytics. In the future, these tools can be used in an automated way to let scientists only work on ready-to-use SciDB arrays to significantly reduce the data management workload for domain scientists. [1] https://github.com/mappl/scidb4geo} and \\url{https://github.com/mappl/scidb4gdal

Need of a consistent and convenient nucleus identification in ENDF files for the automatic construction of the depletion chains

NASA Astrophysics Data System (ADS)

Mosca, Pietro; Mounier, Claude

2016-03-01

The automatic construction of evolution chains recently implemented in GALILEE system is based on the analysis of several ENDF files : the multigroup production cross sections present in the GENDF files processed by NJOY from the ENDF evaluation, the decay file and the fission product yields (FPY) file. In this context, this paper highlights the importance of the nucleus identification to properly interconnect the data mentioned above. The first part of the paper describes the present status of the nucleus identification among the several ENDF files focusing, in particular, on the use of the excited state number and of the isomeric state number. The second part reviews the problems encountered during the automatic construction of the depletion chains using recent ENDF data. The processing of the JEFF-3.1.1, ENDF/B-VII.0 (decay and FPY) and the JEFF-3.2 (production cross section) points out problems about the compliance or not of the nucleus identifiers with the ENDF-6 format and sometimes the inconsistencies among the various ENDF files. In addition, the analysis of EAF-2003 and EAF-2010 shows some incoherence between the ZA product identifier and the reaction identifier MT for the reactions (n, pα) and (n, 2np). As a main result of this work, our suggestion is to change the ENDF format using systematically the isomeric state number to identify the nuclei. This proposal is already compliant to a huge amount ENDF data that are not in agreement with the present ENDF format. This choice is the most convenient because, ultimately, it allows one to give human readable names to the nuclei of the depletion chains.

BOREAS RSS-14 Level-1a GOES-8 Visible, IR and Water Vapor Images

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Newcomer, Jeffrey A.; Faysash, David; Cooper, Harry J.; Smith, Eric A.

2000-01-01

The BOREAS RSS-14 team collected and processed several GOES-7 and GOES-8 image data sets that covered the BOREAS study region. The level-1a GOES-8 images were created by BORIS personnel from the level-1 images delivered by FSU personnel. The data cover 14-Jul-1995 to 21-Sep-1995 and 12-Feb-1996 to 03-Oct-1996. The data start out as three bands with 8-bit pixel values and end up as five bands with 10-bit pixel values. No major problems with the data have been identified. The differences between the level-1 and level-1a GOES-8 data are the formatting and packaging of the data. The images missing from the temporal series of level-1 GOES-8 images were zero-filled by BORIS staff to create files consistent in size and format. In addition, BORIS staff packaged all the images of a given type from a given day into a single file, removed the header information from the individual level-1 files, and placed it into a single descriptive ASCII header file. The data are contained in binary image format files. Due to the large size of the images, the level-1a GOES-8 data are not contained on the BOREAS CD-ROM set. An inventory listing file is supplied on the CD-ROM to inform users of what data were collected. The level-1a GOES-8 image data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). See sections 15 and 16 for more information. The data files are available on a CD-ROM (see document number 20010000884).

Main image file tape description

USGS Publications Warehouse

Warriner, Howard W.

1980-01-01

This Main Image File Tape document defines the data content and file structure of the Main Image File Tape (MIFT) produced by the EROS Data Center (EDC). This document also defines an INQUIRY tape, which is just a subset of the MIFT. The format of the INQUIRY tape is identical to the MIFT except for two records; therefore, with the exception of these two records (described elsewhere in this document), every remark made about the MIFT is true for the INQUIRY tape.

SPICODYN: A Toolbox for the Analysis of Neuronal Network Dynamics and Connectivity from Multi-Site Spike Signal Recordings.

PubMed

Pastore, Vito Paolo; Godjoski, Aleksandar; Martinoia, Sergio; Massobrio, Paolo

2018-01-01

We implemented an automated and efficient open-source software for the analysis of multi-site neuronal spike signals. The software package, named SPICODYN, has been developed as a standalone windows GUI application, using C# programming language with Microsoft Visual Studio based on .NET framework 4.5 development environment. Accepted input data formats are HDF5, level 5 MAT and text files, containing recorded or generated time series spike signals data. SPICODYN processes such electrophysiological signals focusing on: spiking and bursting dynamics and functional-effective connectivity analysis. In particular, for inferring network connectivity, a new implementation of the transfer entropy method is presented dealing with multiple time delays (temporal extension) and with multiple binary patterns (high order extension). SPICODYN is specifically tailored to process data coming from different Multi-Electrode Arrays setups, guarantying, in those specific cases, automated processing. The optimized implementation of the Delayed Transfer Entropy and the High-Order Transfer Entropy algorithms, allows performing accurate and rapid analysis on multiple spike trains from thousands of electrodes.

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

PubMed

Ytow, Nozomi

2016-01-01

The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

Low-energy multiple rendezvous of main belt asteroids

NASA Technical Reports Server (NTRS)

Penzo, Paul A.; Bender, David F.

1992-01-01

An approach to multiple asteroid rendezvous missions to the main belt region is proposed. In this approach key information which consists of a launch date and delta V can be generated for all possible pairs of asteroids satisfying specific constraints. This information is made available on a computer file for 1000 numbered asteroids with reasonable assumptions, limitations, and approximations to limit the computer requirements and the size of the data file.

lcps: Light curve pre-selection

NASA Astrophysics Data System (ADS)

Schlecker, Martin

2018-05-01

lcps searches for transit-like features (i.e., dips) in photometric data. Its main purpose is to restrict large sets of light curves to a number of files that show interesting behavior, such as drops in flux. While lcps is adaptable to any format of time series, its I/O module is designed specifically for photometry of the Kepler spacecraft. It extracts the pre-conditioned PDCSAP data from light curves files created by the standard Kepler pipeline. It can also handle csv-formatted ascii files. lcps uses a sliding window technique to compare a section of flux time series with its surroundings. A dip is detected if the flux within the window is lower than a threshold fraction of the surrounding fluxes.

SEQ-REVIEW: A tool for reviewing and checking spacecraft sequences

NASA Astrophysics Data System (ADS)

Maldague, Pierre F.; El-Boushi, Mekki; Starbird, Thomas J.; Zawacki, Steven J.

1994-11-01

A key component of JPL's strategy to make space missions faster, better and cheaper is the Advanced Multi-Mission Operations System (AMMOS), a ground software intensive system currently in use and in further development. AMMOS intends to eliminate the cost of re-engineering a ground system for each new JPL mission. This paper discusses SEQ-REVIEW, a component of AMMOS that was designed to facilitate and automate the task of reviewing and checking spacecraft sequences. SEQ-REVIEW is a smart browser for inspecting files created by other sequence generation tools in the AMMOS system. It can parse sequence-related files according to a computer-readable version of a 'Software Interface Specification' (SIS), which is a standard document for defining file formats. It lets users display one or several linked files and check simple constraints using a Basic-like 'Little Language'. SEQ-REVIEW represents the first application of the Quality Function Development (QFD) method to sequence software development at JPL. The paper will show how the requirements for SEQ-REVIEW were defined and converted into a design based on object-oriented principles. The process starts with interviews of potential users, a small but diverse group that spans multiple disciplines and 'cultures'. It continues with the development of QFD matrices that related product functions and characteristics to user-demanded qualities. These matrices are then turned into a formal Software Requirements Document (SRD). The process concludes with the design phase, in which the CRC (Class, Responsibility, Collaboration) approach was used to convert requirements into a blueprint for the final product.

SEQ-REVIEW: A tool for reviewing and checking spacecraft sequences

NASA Technical Reports Server (NTRS)

Maldague, Pierre F.; El-Boushi, Mekki; Starbird, Thomas J.; Zawacki, Steven J.

1994-01-01

A key component of JPL's strategy to make space missions faster, better and cheaper is the Advanced Multi-Mission Operations System (AMMOS), a ground software intensive system currently in use and in further development. AMMOS intends to eliminate the cost of re-engineering a ground system for each new JPL mission. This paper discusses SEQ-REVIEW, a component of AMMOS that was designed to facilitate and automate the task of reviewing and checking spacecraft sequences. SEQ-REVIEW is a smart browser for inspecting files created by other sequence generation tools in the AMMOS system. It can parse sequence-related files according to a computer-readable version of a 'Software Interface Specification' (SIS), which is a standard document for defining file formats. It lets users display one or several linked files and check simple constraints using a Basic-like 'Little Language'. SEQ-REVIEW represents the first application of the Quality Function Development (QFD) method to sequence software development at JPL. The paper will show how the requirements for SEQ-REVIEW were defined and converted into a design based on object-oriented principles. The process starts with interviews of potential users, a small but diverse group that spans multiple disciplines and 'cultures'. It continues with the development of QFD matrices that related product functions and characteristics to user-demanded qualities. These matrices are then turned into a formal Software Requirements Document (SRD). The process concludes with the design phase, in which the CRC (Class, Responsibility, Collaboration) approach was used to convert requirements into a blueprint for the final product.

A Pyramid Scheme for Constructing Geologic Maps on Geobrowsers

NASA Astrophysics Data System (ADS)

Whitmeyer, S. J.; de Paor, D. G.; Daniels, J.; Jeremy, N.; Michael, R.; Santangelo, B.

2008-12-01

Hundreds of geologic maps have been draped onto Google Earth (GE) using the ground overlay tag of Keyhole Markup Language (KML) and dozens have been published on academic and survey web pages as downloadable KML or KMZ (zipped KML) files. The vast majority of these are small KML docs that link to single, large - often very large - image files (jpegs, tiffs, etc.) Files that exceed 50 MB in size defeat the purpose of GE as an interactive and responsive, and therefore fast, virtual terrain medium. KML supports super-overlays (a.k.a. image pyramids), which break large graphic files into manageable tiles that load only when they are in the visible region at a sufficient level of detail (LOD), and several automatic tile-generating applications have been written. The process of exporting map data from applications such as ArcGIS® to KML format is becoming more manageable but still poses challenges. Complications arise, for example, because of differences between grid-north at a point on a map and true north at the equivalent location on the virtual globe. In our recent field season, we devised ways of overcoming many of these obstacles in order to generate responsive, panable, zoomable geologic maps in which data is layered in a pyramid structure similar to the image pyramid used for default GE terrain. The structure of our KML code for each level of the pyramid is self-similar: (i) check whether the current tile is in the visible region, (ii) if so, render the current overlay, (iii) add the current data level, and (iv) using four network links, check the visibility and LOD of four nested tiles. By using this pyramid structure we provide the user with access to geologic and map data at multiple levels of observation. For example, when the viewpoint is distant, regional structures and stratigraphy (e.g. lithological groups and terrane boundaries) are visible. As the user zooms to lower elevations, formations and ultimately individual outcrops come into focus. The pyramid structure is ideally suited to geologic data which tends to be unevenly exposed across the earth's surface.

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

Chemopreventive Agent Development | Division of Cancer Prevention

Cancer.gov

[[{"fid":"174","view_mode":"default","fields":{"format":"default","field_file_image_alt_text[und][0][value]":"Chemoprevenentive Agent Development Research Group Homepage Logo","field_file_image_title_text[und][0][value]":"Chemoprevenentive Agent Development Research Group Homepage

17 CFR 16.06 - Errors or omissions.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., reporting markets shall file corrections to errors or omissions in data previously filed with the Commission pursuant to §§ 16.00 and 16.01 in the format and using the coding structure and electronic data submission...

Publications - PR 121 | Alaska Division of Geological & Geophysical Surveys

Science.gov Websites

: Download below or please see our publication sales page for more information. Quadrangle(s): Philip Smith Philip Smith Mountains: Surficial Geology Data File Format File Size Info Download psm-surficial-geo

Publications - RI 2001-1C | Alaska Division of Geological & Geophysical

Science.gov Websites

map of the Chulitna region, southcentral Alaska, scale 1:63,360 (7.5 M) Digital Geospatial Data Digital Geospatial Data Chulitna region surficial geology Data File Format File Size Info Download

Publications - RDF 2015-17 | Alaska Division of Geological & Geophysical

Science.gov Websites

/10.14509/29519 Publication Products Report Report Information rdf2015_017.pdf (347.0 K) Digital Geospatial Data Digital Geospatial Data Tonsina geochemistry: DGGS samples Data File Format File Size Info

VizieR Online Data Catalog: Horizontal temperature at Venus upper atmosphere (Peralta+, 2016)

NASA Astrophysics Data System (ADS)

Peralta, J.; Lopez-Valverde, M. A.; Gilli, G.; Piccialli, A.

2015-11-01

The dayside atmospheric temperatures in the UMLT of Venus (displayed in Figure 7A of this article) are listed as a CSV data file. These values consist of averages in bins of 5° in latitude and 0.25-hours in local time from dayside temperatures covering five years of data (from 2006/05/14 to 2011/06/05). These temperatures were inferred from the CO2 NLTE nadir spectra measured by the instrument VIRTIS-H onboard Venus Express (see article for full description of the procedure), and are representative of the atmospheric region between 10-2 to 10-5mb. Along with the temperatures, we also provide the corresponding error and the number of temperatures averaged in each bin. The format of the CSV file reasonably agrees with the expected format of the data files to be provided in the future version of the Venus International Reference Atmosphere (VIRA). (1 data file).

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

Desktop document delivery using portable document format (PDF) files and the Web.

PubMed Central

Shipman, J P; Gembala, W L; Reeder, J M; Zick, B A; Rainwater, M J

1998-01-01

Desktop access to electronic full-text literature was rated one of the most desirable services in a client survey conducted by the University of Washington Libraries. The University of Washington Health Sciences Libraries (UW HSL) conducted a ten-month pilot test from August 1996 to May 1997 to determine the feasibility of delivering electronic journal articles via the Internet to remote faculty. Articles were scanned into Adobe Acrobat Portable Document Format (PDF) files and delivered to individuals using Multipurpose Internet Mail Extensions (MIME) standard e-mail attachments and the Web. Participants retrieved scanned articles and used the Adobe Acrobat Reader software to view and print files. The pilot test required a special programming effort to automate the client notification and file deletion processes. Test participants were satisfied with the pilot test despite some technical difficulties. Desktop delivery is now offered as a routine delivery method from the UW HSL. PMID:9681165

Desktop document delivery using portable document format (PDF) files and the Web.

PubMed

Shipman, J P; Gembala, W L; Reeder, J M; Zick, B A; Rainwater, M J

1998-07-01

Desktop access to electronic full-text literature was rated one of the most desirable services in a client survey conducted by the University of Washington Libraries. The University of Washington Health Sciences Libraries (UW HSL) conducted a ten-month pilot test from August 1996 to May 1997 to determine the feasibility of delivering electronic journal articles via the Internet to remote faculty. Articles were scanned into Adobe Acrobat Portable Document Format (PDF) files and delivered to individuals using Multipurpose Internet Mail Extensions (MIME) standard e-mail attachments and the Web. Participants retrieved scanned articles and used the Adobe Acrobat Reader software to view and print files. The pilot test required a special programming effort to automate the client notification and file deletion processes. Test participants were satisfied with the pilot test despite some technical difficulties. Desktop delivery is now offered as a routine delivery method from the UW HSL.

"AFacet": a geometry based format and visualizer to support SAR and multisensor signature generation

NASA Astrophysics Data System (ADS)

Rosencrantz, Stephen; Nehrbass, John; Zelnio, Ed; Sudkamp, Beth

2018-04-01

When simulating multisensor signature data (including SAR, LIDAR, EO, IR, etc...), geometry data are required that accurately represent the target. Most vehicular targets can, in real life, exist in many possible configurations. Examples of these configurations might include a rotated turret, an open door, a missing roof rack, or a seat made of metal or wood. Previously we have used the Modelman (.mmp) format and tool to represent and manipulate our articulable models. Unfortunately Modelman is now an unsupported tool and an undocumented binary format. Some work has been done to reverse engineer a reader in Matlab so that the format could continue to be useful. This work was tedious and resulted in an incomplete conversion. In addition, the resulting articulable models could not be altered and re-saved in the Modelman format. The AFacet (.afacet) articulable facet file format is a replacement for the binary Modelman (.mmp) file format. There is a one-time straight forward path for conversion from Modelman to the AFacet format. It is a simple ASCII, comma separated, self-documenting format that is easily readable (and in many cases usefully editable) by a human with any text editor, preventing future obsolescence. In addition, because the format is simple, it is relatively easy for even the most novice programmer to create a program to read and write AFacet files in any language without any special libraries. This paper presents the AFacet format, as well as a suite of tools for creating, articulating, manipulating, viewing, and converting the 370+ (when this paper was written) models that have been converted to the AFacet format.

12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

Code of Federal Regulations, 2012 CFR

2012-01-01

.../Automated Credit Account File Structure This is the structure of the data file to provide information to the... remainder of the data fields defined below should be populated. For data provided in the Sweep/Automated... number. The Account Identifier may be composed of more than one physical data element. If multiple fields...

12 CFR Appendix D to Part 360 - Sweep/Automated Credit Account File Structure

Code of Federal Regulations, 2011 CFR

2011-01-01

.../Automated Credit Account File Structure This is the structure of the data file to provide information to the... remainder of the data fields defined below should be populated. For data provided in the Sweep/Automated... number. The Account Identifier may be composed of more than one physical data element. If multiple fields...