A Mass Spectrometry Proteomics Data Management Platform*

PubMed Central

Sharma, Vagisha; Eng, Jimmy K.; MacCoss, Michael J.; Riffle, Michael

2012-01-01

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are “organically” distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/. PMID:22611296

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.

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.

A Survey of Complex Object Technologies for Digital Libraries

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Argue, Brad; Efron, Miles; Denn, Sheila; Pattuelli, Maria Cristina

2001-01-01

Many early web-based digital libraries (DLs) had implicit assumptions reflected in their architecture that the unit of focus in the DL (frequently "reports" or "e-prints") would only be manifested in a single, or at most a few, common file formats such as PDF or PostScript. DLs have now matured to the point where their contents are commonly no longer simple files. Complex objects in DLs have emerged from in response to various requirements, including: simple aggregation of formats and supporting files, bundling additional information to aid digital preservation, creating opaque digital objects for e-commerce applications, and the incorporation of dynamic services with the traditional data files. We examine a representative (but not necessarily exhaustive) number of current and recent historical web-based complex object technologies and projects that are applicable to DLs: Aurora, Buckets, ComMentor, Cryptolopes, Digibox, Document Management Alliance, FEDORA, Kahn-Wilensky Framework Digital Objects, Metadata Encoding & Transmission Standard, Multivalent Documents, Open eBooks, VERS Encapsulated Objects, and the Warwick Framework.

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

SEGY to ASCII Conversion and Plotting Program 2.0

USGS Publications Warehouse

Goldman, Mark R.

2005-01-01

INTRODUCTION SEGY has long been a standard format for storing seismic data and header information. Almost every seismic processing package can read and write seismic data in SEGY format. In the data processing world, however, ASCII format is the 'universal' standard format. Very few general-purpose plotting or computation programs will accept data in SEGY format. The software presented in this report, referred to as SEGY to ASCII (SAC), converts seismic data written in SEGY format (Barry et al., 1975) to an ASCII data file, and then creates a postscript file of the seismic data using a general plotting package (GMT, Wessel and Smith, 1995). The resulting postscript file may be plotted by any standard postscript plotting program. There are two versions of SAC: one version for plotting a SEGY file that contains a single gather, such as a stacked CDP or migrated section, and a second version for plotting multiple gathers from a SEGY file containing more than one gather, such as a collection of shot gathers. Note that if a SEGY file has multiple gathers, then each gather must have the same number of traces per gather, and each trace must have the same sample interval and number of samples per trace. SAC will read several common standards of SEGY data, including SEGY files with sample values written in either IBM or IEEE floating-point format. In addition, utility programs are present to convert non-standard Seismic Unix (.sux) SEGY files and PASSCAL (.rsy) SEGY files to standard SEGY files. SAC allows complete user control over all plotting parameters including label size and font, tick mark intervals, trace scaling, and the inclusion of a title and descriptive text. SAC shell scripts create a postscript image of the seismic data in vector rather than bitmap format, using GMT's pswiggle command. Although this can produce a very large postscript file, the image quality is generally superior to that of a bitmap image, and commercial programs such as Adobe Illustrator? can manipulate the image more efficiently.

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.

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

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

PubMed

Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

2012-03-01

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Master Metadata Repository and Metadata-Management System

NASA Technical Reports Server (NTRS)

Armstrong, Edward; Reed, Nate; Zhang, Wen

2007-01-01

A master metadata repository (MMR) software system manages the storage and searching of metadata pertaining to data from national and international satellite sources of the Global Ocean Data Assimilation Experiment (GODAE) High Resolution Sea Surface Temperature Pilot Project [GHRSSTPP]. These sources produce a total of hundreds of data files daily, each file classified as one of more than ten data products representing global sea-surface temperatures. The MMR is a relational database wherein the metadata are divided into granulelevel records [denoted file records (FRs)] for individual satellite files and collection-level records [denoted data set descriptions (DSDs)] that describe metadata common to all the files from a specific data product. FRs and DSDs adhere to the NASA Directory Interchange Format (DIF). The FRs and DSDs are contained in separate subdatabases linked by a common field. The MMR is configured in MySQL database software with custom Practical Extraction and Reporting Language (PERL) programs to validate and ingest the metadata records. The database contents are converted into the Federal Geographic Data Committee (FGDC) standard format by use of the Extensible Markup Language (XML). A Web interface enables users to search for availability of data from all sources.

Filtering NetCDF Files by Using the EverVIEW Slice and Dice Tool

USGS Publications Warehouse

Conzelmann, Craig; Romañach, Stephanie S.

2010-01-01

Network Common Data Form (NetCDF) is a self-describing, machine-independent file format for storing array-oriented scientific data. It was created to provide a common interface between applications and real-time meteorological and other 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 surfaced for additional tools to view and manipulate NetCDF datasets, specifically to filter the files by creating subsets of large NetCDF files. The U.S. Geological Survey (USGS) and the Joint Ecosystem Modeling (JEM) group are working to address these needs with applications like the EverVIEW Slice and Dice Tool, which allows users to filter grid-based NetCDF files, thus targeting those data most important to them. The major functions of this tool are as follows: (1) to create subsets of NetCDF files temporally, spatially, and by data value; (2) to view the NetCDF data in table form; and (3) to export the filtered data to a comma-separated value (CSV) file format. The USGS and JEM will continue to work with scientists and natural resource managers across The Everglades to solve complex restoration problems through technological advances.

The Brain/MINDS 3D digital marmoset brain atlas

PubMed Central

Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko

2018-01-01

We present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file format (NIfTI). The atlas can be registered to new data, is useful for connectomics, functional studies, simulation and as a reference. The atlas was based on previously published work but we provide several critical improvements to make this release valuable for researchers. Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres. The data is in the NIfTI format making it easy to integrate into neuroscience pipelines, whereas the previous atlas was in an inaccessible file format. We also provide cortical, mid-cortical and white matter boundary segmentations useful for visualization and analysis. PMID:29437168

Getting the Most Out of Progress Files and Personal Development Planning

ERIC Educational Resources Information Center

Croot, David; Gedye, Sharon

2006-01-01

Progress Files have been set by the government as a specific element of all higher education provision in England and "should consist of two elements: a transcript recording student achievement which should follow a common format devised by institutions collectively through their representative bodies; and a means by which students can …

78 FR 51192 - Secure Supply Chain Pilot Program

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-20

... (PDF) and using the Electronic Common Technical Document (eCTD) format and the Electronic Submissions.... The PDF file name should contain ``3676'' as part of the file name, and the eCTD leaf title should.... For further information regarding eCTD, please refer to the Web site at http://www.fda.gov/Drugs...

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.

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.

Report on IVS-WG4

NASA Astrophysics Data System (ADS)

Gipson, John

2011-07-01

I describe the proposed data structure 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, and also allows for extending the types of data used, e.g., source maps. I discuss the use of the new format in calc/solve and other VLBI analysis packages. I also discuss plans for transitioning to the new structure.

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

PubMed

Pupier, Marion; Nuzillard, Jean-Marc; Wist, Julien; Schlörer, Nils E; Kuhn, Stefan; Erdelyi, Mate; Steinbeck, Christoph; Williams, Antony J; Butts, Craig; Claridge, Tim D W; Mikhova, Bozhana; Robien, Wolfgang; Dashti, Hesam; Eghbalnia, Hamid R; Farès, Christophe; Adam, Christian; Kessler, Pavel; Moriaud, Fabrice; Elyashberg, Mikhail; Argyropoulos, Dimitris; Pérez, Manuel; Giraudeau, Patrick; Gil, Roberto R; Trevorrow, Paul; Jeannerat, Damien

2018-04-14

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases. Copyright © 2018 John Wiley & Sons, Ltd.

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.

Do you also have problems with the file format syndrome?

PubMed

De Cuyper, B; Nyssen, E; Christophe, Y; Cornelis, J

1991-11-01

In a biomedical data processing environment, an essential requirement is the ability to integrate a large class of standard modules for the acquisition, processing and display of the (image) data. Our approach to the management and manipulation of the different data formats is based on the specification of a common standard for the representation of data formats, called 'data nature descriptions' to emphasise that this representation not only specifies the structure but also the contents of data objects (files). The idea behind this concept is to associate each hardware and software component that produces or uses medical data with a description of the data objects manipulated by that component. In our approach a special software module (a format convertor generator) takes care of the appropriate data format conversions, required when two or more components of the system exchange data.

proBAMconvert: A Conversion Tool for proBAM/proBed.

PubMed

Olexiouk, Volodimir; Menschaert, Gerben

2017-07-07

The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface. Furthermore, ProBAMconvert enables information to be output both at the PSM and peptide levels and has a command line interface next to the graphical user interface. Detailed documentation and a completely worked-out tutorial is available at http://probam.biobix.be .

cyvcf2: fast, flexible variant analysis with Python.

PubMed

Pedersen, Brent S; Quinlan, Aaron R

2017-06-15

Variant call format (VCF) files document the genetic variation observed after DNA sequencing, alignment and variant calling of a sample cohort. Given the complexity of the VCF format as well as the diverse variant annotations and genotype metadata, there is a need for fast, flexible methods enabling intuitive analysis of the variant data within VCF and BCF files. We introduce cyvcf2 , a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. bpederse@gmail.com or aaronquinlan@gmail.com. cyvcf2 is available from https://github.com/brentp/cyvcf2 under the MIT license and from common python package managers. Detailed documentation is available at http://brentp.github.io/cyvcf2/. © The Author 2017. Published by Oxford University Press.

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

PubMed Central

O'Boyle, Noel M; Hutchison, Geoffrey R

2008-01-01

Background Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs). Results We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. Conclusion By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit. PMID:19055766

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.

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.

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

ROSAT implementation of a proposed multi-mission x ray data format

NASA Technical Reports Server (NTRS)

Corcoran, M.; Pence, W.; White, R.; Conroy, M.

1992-01-01

Until recently little effort has been made to ensure that data from X-ray telescopes are delivered in a format that reflects the common characteristics that most X-ray datasets share. Instrument-specific data-product design hampers the comparison of X-ray measurements made by different detectors and should be avoided whenever possible. The ROSAT project and the High Energy Astrophysics Science Archive Research Center (HEASARC) have defined a set of X-ray data products ('rationalized files') for ROSAT data that can be used for distribution and archiving of data from other X-ray missions. This set of 'rationalized files' has been defined to isolate instrument-independent and instrument-specific quantities using standards FITS constructs to ensure portability. We discuss the usage of the 'rationalized files' by ROSAT for data distribution and archiving, with particular emphasis on discrimination between instrument-independent and instrument-specific quantities, and discuss application of this format to data from other X-ray missions.

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.

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.

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

PubMed

Abrahamsson, Erik; Plotkin, Steven S

2009-09-01

Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

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.

Collaborative Sharing of Multidimensional Space-time Data Using HydroShare

NASA Astrophysics Data System (ADS)

Gan, T.; Tarboton, D. G.; Horsburgh, J. S.; Dash, P. K.; Idaszak, R.; Yi, H.; Blanton, B.

2015-12-01

HydroShare is a collaborative environment being developed for sharing hydrological data and models. It includes capability to upload data in many formats as resources that can be shared. The HydroShare data model for resources uses a specific format for the representation of each type of data and specifies metadata common to all resource types as well as metadata unique to specific resource types. The Network Common Data Form (NetCDF) was chosen as the format for multidimensional space-time data in HydroShare. NetCDF is widely used in hydrological and other geoscience modeling because it contains self-describing metadata and supports the creation of array-oriented datasets that may include three spatial dimensions, a time dimension and other user defined dimensions. For example, NetCDF may be used to represent precipitation or surface air temperature fields that have two dimensions in space and one dimension in time. This presentation will illustrate how NetCDF files are used in HydroShare. When a NetCDF file is loaded into HydroShare, header information is extracted using the "ncdump" utility. Python functions developed for the Django web framework on which HydroShare is based, extract science metadata present in the NetCDF file, saving the user from having to enter it. Where the file follows Climate Forecast (CF) convention and Attribute Convention for Dataset Discovery (ACDD) standards, metadata is thus automatically populated. Users also have the ability to add metadata to the resource that may not have been present in the original NetCDF file. HydroShare's metadata editing functionality then writes this science metadata back into the NetCDF file to maintain consistency between the science metadata in HydroShare and the metadata in the NetCDF file. This further helps researchers easily add metadata information following the CF and ACDD conventions. Additional data inspection and subsetting functions were developed, taking advantage of Python and command line libraries for working with NetCDF files. We describe the design and implementation of these features and illustrate how NetCDF files from a modeling application may be curated in HydroShare and thus enhance reproducibility of the associated research. We also discuss future development planned for multidimensional space-time data in HydroShare.

ISMRM Raw Data Format: A Proposed Standard for MRI Raw Datasets

PubMed Central

Inati, Souheil J.; Naegele, Joseph D.; Zwart, Nicholas R.; Roopchansingh, Vinai; Lizak, Martin J.; Hansen, David C.; Liu, Chia-Ying; Atkinson, David; Kellman, Peter; Kozerke, Sebastian; Xue, Hui; Campbell-Washburn, Adrienne E.; Sørensen, Thomas S.; Hansen, Michael S.

2015-01-01

Purpose This work proposes the ISMRM Raw Data (ISMRMRD) format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using MRI scanners from four vendors, converted to ISMRMRD format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Results Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. Conclusion The proposed raw data format solves a practical problem for the MRI community. It may serve as a foundation for reproducible research and collaborations. The ISMRMRD format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. PMID:26822475

Capabilities, methodologies, and use of the cambio file-translation application.

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

Lasche, George P.

2007-03-01

This report describes the capabilities, methodologies, and uses of the Cambio computer application, designed to automatically read and display nuclear spectral data files of any known format in the world and to convert spectral data to one of several commonly used analysis formats. To further assist responders, Cambio incorporates an analysis method based on non-linear fitting techniques found in open literature and implemented in openly published source code in the late 1980s. A brief description is provided of how Cambio works, of what basic formats it can currently read, and how it can be used. Cambio was developed at Sandiamore » National Laboratories and is provided as a free service to assist nuclear emergency response analysts anywhere in the world in the fight against nuclear terrorism.« less

78 FR 24465 - Ballard Terminal Railroad Company, L.L.C.-Acquisition and Operation Exemption-Woodinville...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-25

... National Trails System Act, 16 U.S.C. 1247(d). Ballard also seeks the right to provide common carrier rail... use negotiations under 16 U.S.C. 1247(d).\\2\\ The Board seeks comments from interested persons on... submitted either via the Board's e-filing format or in the traditional paper format. Any person using e...

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.

Batch Conversion of 1-D FITS Spectra to Common Graphical Display Files

NASA Astrophysics Data System (ADS)

MacConnell, Darrell J.; Patterson, A. P.; Wing, R. F.; Costa, E.; Jedrzejewski, R. I.

2008-09-01

Authors DJM, RFW, and EC have accumulated about 1000 spectra of cool stars from CTIO, ESO, and LCO over the interval 1985 to 1994 and processed them with the standard IRAF tasks into FITS files of normalized intensity vs. wavelength. With the growth of the Web as a means of exchanging and preserving scientific information, we desired to put the spectra into a Web-readable format. We have searched without success sites such as the Goddard FITS Image Viewer page, http://fits.gsfc.nasa.gov/fits_viewer.html, for a program to convert a large number of 1-d stellar spectra from FITS format into common formats such as PDF, PS, or PNG. Author APP has written a Python script to do this using the PyFITS module and plotting routines from Pylab. The program determines the wavelength calibration using header keywords and creates PNG plots with a legend read from a CSV file that may contain the star name, position, spectral type, etc. It could readily be adapted to perform almost any kind of simple batch processing of astronomical data. The program may be obtained from the first author (jack@stsci.edu). Support for DJM from the research program for CSC astronomers at STScI is gratefully acknowledged. The Space Telescope Science Institute is operated by the Association of Universities for Research in Astronomy Inc. under NASA contract NAS 5-26555.

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 .

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.

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.

Enhanced Historical Land-Use and Land-Cover Data Sets of the U.S. Geological Survey

USGS Publications Warehouse

Price, Curtis V.; Nakagaki, Naomi; Hitt, Kerie J.; Clawges, Rick M.

2007-01-01

Historical land-use and land-cover data, available from the U.S. Geological Survey (USGS) for the conterminous United States and Hawaii, have been enhanced for use in geographic information systems (GIS) applications. The original digital data sets were created by the USGS in the late 1970s and early 1980s and were later converted by USGS and the U.S. Environmental Protection Agency (USEPA) to a geographic information system (GIS) format in the early 1990s. These data were made available on USEPA's Web site since the early 1990s and have been used for many national applications, despite minor coding and topological errors. During the 1990s, a group of USGS researchers made modifications to the data set for use in the National Water-Quality Assessment Program. These edited files have been further modified to create a more accurate, topologically clean, and seamless national data set. Several different methods, including custom editing software and several batch processes, were applied to create this enhanced version of the national data set. The data sets are included in this report in the commonly used shapefile and Tagged Image Format File (TIFF) formats. In addition, this report includes two polygon data sets (in shapefile format) representing (1) land-use and land-cover source documentation extracted from the previously published USGS data files, and (2) the extent of each polygon data file.

Web servlet-assisted, dial-in flow cytometry data analysis.

PubMed

Battye, F

2001-02-01

The obvious benefits of centralized data storage notwithstanding, the size of modern flow cytometry data files discourages their transmission over commonly used telephone modem connections. The proposed solution is to install at the central location a web servlet that can extract compact data arrays, of a form dependent on the requested display type, from the stored files and transmit them to a remote client computer program for display. A client program and a web servlet, both written in the Java programming language, were designed to communicate over standard network connections. The client program creates familiar numerical and graphical display types and allows the creation of gates from combinations of user-defined regions. Data compression techniques further reduce transmission times for data arrays that are already much smaller than the data file itself. For typical data files, network transmission times were reduced more than 700-fold for extraction of one-dimensional (1-D) histograms, between 18 and 120-fold for 2-D histograms, and 6-fold for color-coded dot plots. Numerous display formats are possible without further access to the data file. This scheme enables telephone modem access to centrally stored data without restricting flexibility of display format or preventing comparisons with locally stored files. Copyright 2001 Wiley-Liss, Inc.

Linking netCDF Data with the Semantic Web - Enhancing Data Discovery Across Domains

NASA Astrophysics Data System (ADS)

Biard, J. C.; Yu, J.; Hedley, M.; Cox, S. J. D.; Leadbetter, A.; Car, N. J.; Druken, K. A.; Nativi, S.; Davis, E.

2016-12-01

Geophysical data communities are publishing large quantities of data across a wide variety of scientific domains which are overlapping more and more. Whilst netCDF is a common format for many of these communities, it is only one of a large number of data storage and transfer formats. One of the major challenges ahead is finding ways to leverage these diverse data sets to advance our understanding of complex problems. We describe a methodology for incorporating Resource Description Framework (RDF) triples into netCDF files called netCDF-LD (netCDF Linked Data). NetCDF-LD explicitly connects the contents of netCDF files - both data and metadata, with external web-based resources, including vocabularies, standards definitions, and data collections, and through them, a whole host of related information. This approach also preserves and enhances the self describing essence of the netCDF format and its metadata, whilst addressing the challenge of integrating various conventions into files. We present a case study illustrating how reasoning over RDF graphs can empower researchers to discover datasets across domain boundaries.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

LANL Summer 2016 Report

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

Mendoza, Paul Michael

The Monte Carlo N-Particle (MCNP) transport code developed at Los Alamos National Laboratory (LANL) utilizes nuclear cross-section data in a compact ENDF (ACE) format. The accuracy of MCNP calculations depends on the accuracy of nuclear ACE data tables, which depends on the accuracy of the original ENDF files. There are some noticeable differences in ENDF files from one generation to the next, even among the more common fissile materials. As the next generation of ENDF files is being prepared, several software tools were developed to simulate a large number of benchmarks in MCNP (over 1000), collect data from these simulations,more » and visually represent the results.« less

Informatics in radiology (infoRAD): free DICOM image viewing and processing software for the Macintosh computer: what's available and what it can do for you.

PubMed

Escott, Edward J; Rubinstein, David

2004-01-01

It is often necessary for radiologists to use digital images in presentations and conferences. Most imaging modalities produce images in the Digital Imaging and Communications in Medicine (DICOM) format. The image files tend to be large and thus cannot be directly imported into most presentation software, such as Microsoft PowerPoint; the large files also consume storage space. There are many free programs that allow viewing and processing of these files on a personal computer, including conversion to more common file formats such as the Joint Photographic Experts Group (JPEG) format. Free DICOM image viewing and processing software for computers running on the Microsoft Windows operating system has already been evaluated. However, many people use the Macintosh (Apple Computer) platform, and a number of programs are available for these users. The World Wide Web was searched for free DICOM image viewing or processing software that was designed for the Macintosh platform or is written in Java and is therefore platform independent. The features of these programs and their usability were evaluated. There are many free programs for the Macintosh platform that enable viewing and processing of DICOM images. (c) RSNA, 2004.

Implementing Network Common Data Form (netCDF) for the 3DWF Model

DTIC Science & Technology

2016-02-01

format. In addition, data extraction from netCDF-formatted Weather Research and Forecasting ( WRF ) model results necessary for the 3DWF model’s wind...Requirement for the 3DWF Model 1 3. Implementing netCDF to the 3DWF Model 2 3.1 Weather Research and Forecasting ( WRF ) domain and results 3 3.2...Extracting Variables from netCDF Formatted WRF Data File 5 3.3 Converting the 3DWF’s Results into netCDF 11 4. Conclusion 14 5. References 15 Appendix

Geographic Information for Analysis of Highway Runoff-Quality Data on a National or Regional Scale in the Conterminous United States

USGS Publications Warehouse

Smieszek, Tomas W.; Granato, Gregory E.

2000-01-01

Spatial data are important for interpretation of water-quality information on a regional or national scale. Geographic information systems (GIS) facilitate interpretation and integration of spatial data. The geographic information and data compiled for the conterminous United States during the National Highway Runoff Water-Quality Data and Methodology Synthesis project is described in this document, which also includes information on the structure, file types, and the geographic information in the data files. This 'geodata' directory contains two subdirectories, labeled 'gisdata' and 'gisimage.' The 'gisdata' directory contains ArcInfo coverages, ArcInfo export files, shapefiles (used in ArcView), Spatial Data Transfer Standard Topological Vector Profile format files, and meta files in subdirectories organized by file type. The 'gisimage' directory contains the GIS data in common image-file formats. The spatial geodata includes two rain-zone region maps and a map of national ecosystems originally published by the U.S. Environmental Protection Agency; regional estimates of mean annual streamflow, and water hardness published by the Federal Highway Administration; and mean monthly temperature, mean annual precipitation, and mean monthly snowfall modified from data published by the National Climatic Data Center and made available to the public by the Oregon Climate Service at Oregon State University. These GIS files were compiled for qualitative spatial analysis of available data on a national and(or) regional scale and therefore should be considered as qualitative representations, not precise geographic location 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

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...

Public-domain-software solution to data-access problems for numerical modelers

USGS Publications Warehouse

Jenter, Harry; Signell, Richard

1992-01-01

Unidata's network Common Data Form, netCDF, provides users with an efficient set of software for scientific-data-storage, retrieval, and manipulation. The netCDF file format is machine-independent, direct-access, self-describing, and in the public domain, thereby alleviating many problems associated with accessing output from large hydrodynamic models. NetCDF has programming interfaces in both the Fortran and C computer language with an interface to C++ planned for release in the future. NetCDF also has an abstract data type that relieves users from understanding details of the binary file structure; data are written and retrieved by an intuitive, user-supplied name rather than by file position. Users are aided further by Unidata's inclusion of the Common Data Language, CDL, a printable text-equivalent of the contents of a netCDF file. Unidata provides numerous operators and utilities for processing netCDF files. In addition, a number of public-domain and proprietary netCDF utilities from other sources are available at this time or will be available later this year. The U.S. Geological Survey has produced and is producing a number of public-domain netCDF utilities.

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 ...

Use of Schema on Read in Earth Science Data Archives

NASA Astrophysics Data System (ADS)

Petrenko, M.; Hegde, M.; Smit, C.; Pilone, P.; Pham, L.

2017-12-01

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—spatial or temporal—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 support for "schema-on-read" used for data access, and common use cases covering data usage patterns seen in a geospatial data archive.

78 FR 50396 - Common Format for Federal Entity Transition Plans

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-19

..., Associate Administrator, Office of Spectrum Management. [FR Doc. 2013-20149 Filed 8-16-13; 8:45 am] BILLING..., Office of Spectrum Management. Each commenter should include the name of the person or organization... Spectrum Management, National Telecommunications and Information Administration, U.S. Department of...

Common Pitfalls in F77 Code Conversion

DTIC Science & Technology

2003-02-01

implementation versus another are the source of these errors rather than typography . It is well to use the practice of commenting-out original source file lines...identifier), every I in the format field must be replaced with f followed by an appropriate floating point format designator . Floating point numeric...helps even more. Finally, libraries are a major source of non-portablility[sic], with graphics libraries one of the chief culprits. We in Fusion

46 CFR 531.9 - Publication.

Code of Federal Regulations, 2013 CFR

2013-10-01

... NSAs under this part are also required to make available to the public, contemporaneously with the filing of each NSA with the Commission, and in tariff format, a concise statement of the following... not be made to a tariff of a common carrier other than the NVOCC party to the NSA. (c) Location. The...

46 CFR 531.9 - Publication.

Code of Federal Regulations, 2010 CFR

2010-10-01

... NSAs under this part are also required to make available to the public, contemporaneously with the filing of each NSA with the Commission, and in tariff format, a concise statement of the following... not be made to a tariff of a common carrier other than the NVOCC party to the NSA. (c) Location. The...

46 CFR 531.9 - Publication.

Code of Federal Regulations, 2014 CFR

2014-10-01

... NSAs under this part are also required to make available to the public, contemporaneously with the filing of each NSA with the Commission, and in tariff format, a concise statement of the following... not be made to a tariff of a common carrier other than the NVOCC party to the NSA. (c) Location. The...

46 CFR 531.9 - Publication.

Code of Federal Regulations, 2011 CFR

2011-10-01

... NSAs under this part are also required to make available to the public, contemporaneously with the filing of each NSA with the Commission, and in tariff format, a concise statement of the following... not be made to a tariff of a common carrier other than the NVOCC party to the NSA. (c) Location. The...

46 CFR 531.9 - Publication.

Code of Federal Regulations, 2012 CFR

2012-10-01

... NSAs under this part are also required to make available to the public, contemporaneously with the filing of each NSA with the Commission, and in tariff format, a concise statement of the following... not be made to a tariff of a common carrier other than the NVOCC party to the NSA. (c) Location. The...

Common Bibliographic Standards for Baylor University Libraries. Revised.

ERIC Educational Resources Information Center

Scott, Sharon; And Others

Developed by a Baylor University (Texas) Task Force, the revised policies of bibliographic standards for the university libraries provide formats for: (1) archives and manuscript control; (2) audiovisual media; (3) books; (4) machine-readable data files; (5) maps; (6) music scores; (7) serials; and (8) sound recordings. The task force assumptions…

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.

ISMRM Raw data format: A proposed standard for MRI raw datasets.

PubMed

Inati, Souheil J; Naegele, Joseph D; Zwart, Nicholas R; Roopchansingh, Vinai; Lizak, Martin J; Hansen, David C; Liu, Chia-Ying; Atkinson, David; Kellman, Peter; Kozerke, Sebastian; Xue, Hui; Campbell-Washburn, Adrienne E; Sørensen, Thomas S; Hansen, Michael S

2017-01-01

This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. A file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411-421, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

Team X Spacecraft Instrument Database Consolidation

NASA Technical Reports Server (NTRS)

Wallenstein, Kelly A.

2005-01-01

In the past decade, many changes have been made to Team X's process of designing each spacecraft, with the purpose of making the overall procedure more efficient over time. One such improvement is the use of information databases from previous missions, designs, and research. By referring to these databases, members of the design team can locate relevant instrument data and significantly reduce the total time they spend on each design. The files in these databases were stored in several different formats with various levels of accuracy. During the past 2 months, efforts have been made in an attempt to combine and organize these files. The main focus was in the Instruments department, where spacecraft subsystems are designed based on mission measurement requirements. A common database was developed for all instrument parameters using Microsoft Excel to minimize the time and confusion experienced when searching through files stored in several different formats and locations. By making this collection of information more organized, the files within them have become more easily searchable. Additionally, the new Excel database offers the option of importing its contents into a more efficient database management system in the future. This potential for expansion enables the database to grow and acquire more search features as needed.

Volcanic observation data and simulation database at NIED, Japan (Invited)

NASA Astrophysics Data System (ADS)

Fujita, E.; Ueda, H.; Kozono, T.

2009-12-01

NIED (Nat’l Res. Inst. for Earth Sci. & Disast. Prev.) has a project to develop two volcanic database systems: (1) volcanic observation database; (2) volcanic simulation database. The volcanic observation database is the data archive center obtained by the geophysical observation networks at Mt. Fuji, Miyake, Izu-Oshima, Iwo-jima and Nasu volcanoes, central Japan. The data consist of seismic (both high-sensitivity and broadband), ground deformation (tiltmeter, GPS) and those from other sensors (e.g., rain gauge, gravimeter, magnetometer, pressure gauge.) These data is originally stored in “WIN format,” the Japanese standard format, which is also at the Hi-net (High sensitivity seismic network Japan, http://www.hinet.bosai.go.jp/). NIED joins to WOVOdat and we have prepared to upload our data, via XML format. Our concept of the XML format is 1)a common format for intermediate files to upload into the WOVOdat DB, 2) for data files downloaded from the WOVOdat DB, 3) for data exchanges between observatories without the WOVOdat DB, 4) for common data files in each observatory, 5) for data communications between systems and softwares and 6)a for softwares. NIED is now preparing for (2) the volcanic simulation database. The objective of this project is to support to develop a “real-time” hazard map, i.e., the system which is effective to evaluate volcanic hazard in case of emergency, including the up-to-date conditions. Our system will include lava flow simulation (LavaSIM) and pyroclastic flow simulation (grvcrt). The database will keep many cases of assumed simulations and we can pick up the most probable case as the first evaluation in case the eruption started. The final goals of the both database will realize the volcanic eruption prediction and forecasting in real time by the combination of monitoring data and numerical simulations.

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.

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

PCF File Format.

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

Thoreson, Gregory G

PCF files are binary files designed to contain gamma spectra and neutron count rates from radiation sensors. It is the native format for the GAmma Detector Response and Analysis Software (GADRAS) package [1]. It can contain multiple spectra and information about each spectrum such as energy calibration. This document outlines the format of the file that would allow one to write a computer program to parse and write such files.

Automatic meta-data collection of STP observation data

NASA Astrophysics Data System (ADS)

Ishikura, S.; Kimura, E.; Murata, K.; Kubo, T.; Shinohara, I.

2006-12-01

For the geo-science and the STP (Solar-Terrestrial Physics) studies, various observations have been done by satellites and ground-based observatories up to now. These data are saved and managed at many organizations, but no common procedure and rule to provide and/or share these data files. Researchers have felt difficulty in searching and analyzing such different types of data distributed over the Internet. To support such cross-over analyses of observation data, we have developed the STARS (Solar-Terrestrial data Analysis and Reference System). The STARS consists of client application (STARS-app), the meta-database (STARS- DB), the portal Web service (STARS-WS) and the download agent Web service (STARS DLAgent-WS). The STARS-DB includes directory information, access permission, protocol information to retrieve data files, hierarchy information of mission/team/data and user information. Users of the STARS are able to download observation data files without knowing locations of the files by using the STARS-DB. We have implemented the Portal-WS to retrieve meta-data from the meta-database. One reason we use the Web service is to overcome a variety of firewall restrictions which is getting stricter in recent years. Now it is difficult for the STARS client application to access to the STARS-DB by sending SQL query to obtain meta- data from the STARS-DB. Using the Web service, we succeeded in placing the STARS-DB behind the Portal- WS and prevent from exposing it on the Internet. The STARS accesses to the Portal-WS by sending the SOAP (Simple Object Access Protocol) request over HTTP. Meta-data is received as a SOAP Response. The STARS DLAgent-WS provides clients with data files downloaded from data sites. The data files are provided with a variety of protocols (e.g., FTP, HTTP, FTPS and SFTP). These protocols are individually selected at each site. The clients send a SOAP request with download request messages and receive observation data files as a SOAP Response with DIME-Attachment. By introducing the DLAgent-WS, we overcame the problem that the data management policies of each data site are independent. Another important issue to be overcome is how to collect the meta-data of observation data files. So far, STARS-DB managers have added new records to the meta-database and updated them manually. We have had a lot of troubles to maintain the meta-database because observation data are generated every day and the quantity of data files increases explosively. For that purpose, we have attempted to automate collection of the meta-data. In this research, we adopted the RSS 1.0 (RDF Site Summary) as a format to exchange meta-data in the STP fields. The RSS is an RDF vocabulary that provides a multipurpose extensible meta-data description and is suitable for syndication of meta-data. Most of the data in the present study are described in the CDF (Common Data Format), which is a self- describing data format. We have converted meta-information extracted from the CDF data files into RSS files. The program to generate the RSS files is executed on data site server once a day and the RSS files provide information of new data files. The RSS files are collected by RSS collection server once a day and the meta- data are stored in the STARS-DB.

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

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...

Managing the computational chemistry big data problem: the ioChem-BD platform.

PubMed

Álvarez-Moreno, M; de Graaf, C; López, N; Maseras, F; Poblet, J M; Bo, C

2015-01-26

We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media.

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.

AADL Fault Modeling and Analysis Within an ARP4761 Safety Assessment

DTIC Science & Technology

2014-10-01

Analysis Generator 27 3.2.3 Mapping to OpenFTA Format File 27 3.2.4 Mapping to Generic XML Format 28 3.2.5 AADL and FTA Mapping Rules 28 3.2.6 Issues...PSSA), System Safety Assessment (SSA), Common Cause Analysis (CCA), Fault Tree Analysis ( FTA ), Failure Modes and Effects Analysis (FMEA), Failure...Modes and Effects Summary, Mar - kov Analysis (MA), and Dependence Diagrams (DDs), also referred to as Reliability Block Dia- grams (RBDs). The

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

Dagik: A Quick Look System of the Geospace Data in KML format

NASA Astrophysics Data System (ADS)

Yoshida, D.; Saito, A.

2007-12-01

Dagik (Daily Geospace data in KML) is a quick look plot sharing system using Google Earth as a data browser. It provides daily data lists that contain network links to the KML/KMZ files of various geospace data. KML is a markup language to display data on Google Earth, and KMZ is a compressed file of KML. Users can browse the KML/KMZ files with the following procedures: 1) download "dagik.kml" from Dagik homepage (http://www- step.kugi.kyoto-u.ac.jp/dagik/), and open it with Google Earth, 2) select date, 3) select data type to browse. Dagik is a collection of network links to KML/KMZ files. The daily Dagik files are available since 1957, though they contain only the geomagnetic index data in the early periods. There are three activities of Dagik. The first one is the generation of the daily data lists, the second is to provide several useful tools, such as observatory lists, and the third is to assist researchers to make KML/KMZ data plots. To make the plot browsing easy, there are three rules for Dagik plot format: 1) one file contains one UT day data, 2) use common plot panel size, 3) share the data list. There are three steps to join Dagik as a plot provider: 1) make KML/KMZ files of the data, 2) put the KML/KMZ files on Web, 3) notice Dagik group the URL address and description of the files. The KML/KMZ files will be included in Dagik data list. As of September 2007, quick looks of several geosphace data, such as GPS total electron content data, ionosonde data, magnetometer data, FUV imaging data by a satellite, ground-based airglow data, and satellite footprint data, are available. The system of Dagik is introduced in the presentation. u.ac.jp/dagik/

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.

PSTOOLS - FOUR PROGRAMS THAT INTERPRET/FORMAT POSTSCRIPT FILES

NASA Technical Reports Server (NTRS)

Choi, D.

1994-01-01

PSTOOLS is a package of four programs that operate on files written in the page description language, PostScript. The programs include a PostScript previewer for the IRIS workstation, a PostScript driver for the Matrix QCRZ film recorder, a PostScript driver for the Tektronix 4693D printer, and a PostScript code beautifier that formats PostScript files to be more legible. The three programs PSIRIS, PSMATRIX, and PSTEK are similar in that they all interpret the PostScript language and output the graphical results to a device, and they support color PostScript images. The common code which is shared by these three programs is included as a library of routines. PSPRETTY formats a PostScript file by appropriately indenting procedures and code delimited by "saves" and "restores." PSTOOLS does not use Adobe fonts. PSTOOLS is written in C-language for implementation on SGI IRIS 4D series workstations running IRIX 3.2 or later. A README file and UNIX man pages provide information regarding the installation and use of the PSTOOLS programs. A six-page manual which provides slightly more detailed information may be purchased separately. The standard distribution medium for this package is one .25 inch streaming magnetic tape cartridge in UNIX tar format. PSIRIS (the largest program) requires 1.2Mb of main memory. PSMATRIX requires the "gpib" board (IEEE 488) available from Silicon Graphics. Inc. The programs with graphical interfaces require that the IRIS have at least 24 bit planes. This package was developed in 1990 and updated in 1991. SGI, IRIS 4D, and IRIX are trademarks of Silicon Graphics, Inc. Matrix QCRZ is a registered trademark of the AGFA Group. Tektronix 4693D is a trademark of Tektronix, Inc. Adobe is a trademark of Adobe Systems Incorporated. PostScript is a registered trademark of Adobe Systems Incorporated. UNIX is a registered trademark of AT&T Bell Laboratories.

The digital geologic map of Colorado in ARC/INFO format, Part B. Common files

USGS Publications Warehouse

Green, Gregory N.

1992-01-01

This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map. This database was developed on a MicroVAX computer system using VAX V 5.4 nd ARC/INFO 5.0 software. UPDATE: April 1995, The update was done solely for the purpose of adding the abilitly to plot to an HP650c plotter. Two new ARC/INFO plot AMLs along with a lineset and shadeset for the HP650C design jet printer have been included. These new files are COLORADO.650, INDEX.650, TWETOLIN.E00 and TWETOSHD.E00. These files were created on a UNIX platform with ARC/INFO 6.1.2. Updated versions of INDEX.E00, CONTACT.E00, LINE.E00, DECO.E00 and BORDER.E00 files that included the newly defined HP650c items are also included. * Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Descriptors: The Digital Geologic Map of Colorado in ARC/INFO Format Open-File Report 92-050

MDplot: Visualise Molecular Dynamics.

PubMed

Margreitter, Christian; Oostenbrink, Chris

2017-05-10

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

Sideloading - Ingestion of Large Point Clouds Into the Apache Spark Big Data Engine

NASA Astrophysics Data System (ADS)

Boehm, J.; Liu, K.; Alis, C.

2016-06-01

In the geospatial domain we have now reached the point where data volumes we handle have clearly grown beyond the capacity of most desktop computers. This is particularly true in the area of point cloud processing. It is therefore naturally lucrative to explore established big data frameworks for big geospatial data. The very first hurdle is the import of geospatial data into big data frameworks, commonly referred to as data ingestion. Geospatial data is typically encoded in specialised binary file formats, which are not naturally supported by the existing big data frameworks. Instead such file formats are supported by software libraries that are restricted to single CPU execution. We present an approach that allows the use of existing point cloud file format libraries on the Apache Spark big data framework. We demonstrate the ingestion of large volumes of point cloud data into a compute cluster. The approach uses a map function to distribute the data ingestion across the nodes of a cluster. We test the capabilities of the proposed method to load billions of points into a commodity hardware compute cluster and we discuss the implications on scalability and performance. The performance is benchmarked against an existing native Apache Spark data import implementation.

Intelligent Patching of Conceptual Geometry for CFD Analysis

NASA Technical Reports Server (NTRS)

Li, Wu

2010-01-01

The iPatch computer code for intelligently patching surface grids was developed to convert conceptual geometry to computational fluid dynamics (CFD) geometry (see figure). It automatically uses bicubic B-splines to extrapolate (if necessary) each surface in a conceptual geometry so that all the independently defined geometric components (such as wing and fuselage) can be intersected to form a watertight CFD geometry. The software also computes the intersection curves of surface patches at any resolution (up to 10.4 accuracy) specified by the user, and it writes the B-spline surface patches, and the corresponding boundary points, for the watertight CFD geometry in the format that can be directly used by the grid generation tool VGRID. iPatch requires that input geometry be in PLOT3D format where each component surface is defined by a rectangular grid {(x(i,j), y(i,j), z(i,j)):1less than or equal to i less than or equal to m, 1 less than or equal to j less than or equal to n} that represents a smooth B-spline surface. All surfaces in the PLOT3D file conceptually represent a watertight geometry of components of an aircraft on the half-space y greater than or equal to 0. Overlapping surfaces are not allowed, but could be fixed by a utility code "fixp3d". The fixp3d utility code first finds the two grid lines on the two surface grids that are closest to each other in Hausdorff distance (a metric to measure the discrepancies of two sets); then uses one of the grid lines as the transition line, extending grid lines on one grid to the other grid to form a merged grid. Any two connecting surfaces shall have a "visually" common boundary curve, or can be described by an intersection relationship defined in a geometry specification file. The intersection of two surfaces can be at a conceptual level. However, the intersection is directional (along either i or j index direction), and each intersecting grid line (or its spine extrapolation) on the first surface should intersect the second surface. No two intersection relationships will result in a common intersection point of three surfaces. The output files of iPatch are IGES, d3m, and mapbc files that define the CFD geometry in VGRID format. The IGES file gives the NURBS definition of the outer mold line in the geometry. The d3m file defines how the outer mold line is broken into surface patches whose boundary curves are defined by points. The mapbc file specifies what the boundary condition is on each patch and the corresponding NURBS surface definition of each non-planar patch in the IGES file.

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

PubMed

Barnett, Derek W; Garrison, Erik K; Quinlan, Aaron R; Strömberg, Michael P; Marth, Gabor T

2011-06-15

Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

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...

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.

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.

The NeXus data format.

PubMed

Könnecke, Mark; Akeroyd, Frederick A; Bernstein, Herbert J; Brewster, Aaron S; Campbell, Stuart I; Clausen, Björn; Cottrell, Stephen; Hoffmann, Jens Uwe; Jemian, Pete R; Männicke, David; Osborn, Raymond; Peterson, Peter F; Richter, Tobias; Suzuki, Jiro; Watts, Benjamin; Wintersberger, Eugen; Wuttke, Joachim

2015-02-01

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.

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.

ISTP CDF Skeleton Editor

NASA Technical Reports Server (NTRS)

Chimiak, Reine; Harris, Bernard; Williams, Phillip

2013-01-01

Basic Common Data Format (CDF) tools (e.g., cdfedit) provide no specific support for creating International Solar-Terrestrial Physics/Space Physics Data Facility (ISTP/SPDF) standard files. While it is possible for someone who is familiar with the ISTP/SPDF metadata guidelines to create compliant files using just the basic tools, the process is error-prone and unreasonable for someone without ISTP/SPDF expertise. The key problem is the lack of a tool with specific support for creating files that comply with the ISTP/SPDF guidelines. There are basic CDF tools such as cdfedit and skeletoncdf for creating CDF files, but these have no specific support for creating ISTP/ SPDF compliant files. The SPDF ISTP CDF skeleton editor is a cross-platform, Java-based GUI editor program that allows someone with only a basic understanding of the ISTP/SPDF guidelines to easily create compliant files. The editor is a simple graphical user interface (GUI) application for creating and editing ISTP/SPDF guideline-compliant skeleton CDF files. The SPDF ISTP CDF skeleton editor consists of the following components: A swing-based Java GUI program, JavaHelp-based manual/ tutorial, Image/Icon files, and HTML Web page for distribution. The editor is available as a traditional Java desktop application as well as a Java Network Launching Protocol (JNLP) application. Once started, it functions like a typical Java GUI file editor application for creating/editing application-unique files.

UniGene Tabulator: a full parser for the UniGene format.

PubMed

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

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.

Novel 3D Compression Methods for Geometry, Connectivity and Texture

NASA Astrophysics Data System (ADS)

Siddeq, M. M.; Rodrigues, M. A.

2016-06-01

A large number of applications in medical visualization, games, engineering design, entertainment, heritage, e-commerce and so on require the transmission of 3D models over the Internet or over local networks. 3D data compression is an important requirement for fast data storage, access and transmission within bandwidth limitations. The Wavefront OBJ (object) file format is commonly used to share models due to its clear simple design. Normally each OBJ file contains a large amount of data (e.g. vertices and triangulated faces, normals, texture coordinates and other parameters) describing the mesh surface. In this paper we introduce a new method to compress geometry, connectivity and texture coordinates by a novel Geometry Minimization Algorithm (GM-Algorithm) in connection with arithmetic coding. First, each vertex ( x, y, z) coordinates are encoded to a single value by the GM-Algorithm. Second, triangle faces are encoded by computing the differences between two adjacent vertex locations, which are compressed by arithmetic coding together with texture coordinates. We demonstrate the method on large data sets achieving compression ratios between 87 and 99 % without reduction in the number of reconstructed vertices and triangle faces. The decompression step is based on a Parallel Fast Matching Search Algorithm (Parallel-FMS) to recover the structure of the 3D mesh. A comparative analysis of compression ratios is provided with a number of commonly used 3D file formats such as VRML, OpenCTM and STL highlighting the performance and effectiveness of the proposed method.

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.

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...

The crystalline sponge method: MOF terminal ligand effects† †Electronic supplementary information (ESI) available: Experimental and crystallographic procedures, and data tables. CCDC 1063685 and 1063686. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5cc03840e Click here for additional data file. Click here for additional data file.

PubMed Central

Ramadhar, Timothy R.; Zheng, Shao-Liang; Chen, Yu-Sheng

2015-01-01

Bromide and chloride analogs of the commonly used zinc iodide-based metal organic framework for the crystalline sponge method were synthesized and evaluated. Inclusion of (1R)-(–)-menthyl acetate into these MOFs was analysed using third-generation synchrotron radiation, and the effects and potential benefits of varying the MOF terminal ligand are discussed. PMID:26081991

HEPDOOP: High-Energy Physics Analysis using Hadoop

NASA Astrophysics Data System (ADS)

Bhimji, W.; Bristow, T.; Washbrook, A.

2014-06-01

We perform a LHC data analysis workflow using tools and data formats that are commonly used in the "Big Data" community outside High Energy Physics (HEP). These include Apache Avro for serialisation to binary files, Pig and Hadoop for mass data processing and Python Scikit-Learn for multi-variate analysis. Comparison is made with the same analysis performed with current HEP tools in ROOT.

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...

BamTools: a C++ API and toolkit for analyzing and managing BAM files

PubMed Central

Barnett, Derek W.; Garrison, Erik K.; Quinlan, Aaron R.; Strömberg, Michael P.; Marth, Gabor T.

2011-01-01

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools. Contact: barnetde@bc.edu PMID:21493652

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

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.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

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.

MDplot: Visualise Molecular Dynamics

PubMed Central

Margreitter, Christian; Oostenbrink, Chris

2017-01-01

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package′s functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. Availability The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project′s GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license. PMID:28845302

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 NeXus data format

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

Könnecke, Mark; Akeroyd, Frederick A.; Bernstein, Herbert J.

2015-01-30

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitionsmore » for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.« less

The NeXus data format

DOE PAGES

Könnecke, Mark; Akeroyd, Frederick A.; Bernstein, Herbert J.; ...

2015-01-30

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitionsmore » for the exchange of data between applications. As a result, NeXus provides structures for raw experimental data as well as for processed data.« less

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.

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.

The XBabelPhish MAGE-ML and XML translator.

PubMed

Maier, Don; Wymore, Farrell; Sherlock, Gavin; Ball, Catherine A

2008-01-18

MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE-ML files are exceptionally large - too large to be easily read by most people, and often too large to be read by most software programs. Second, the MAGE-ML standard permits many ways of representing the same information. As a result, different producers of MAGE-ML create different documents describing the same experiment and its data. Recognizing all the variants is an unwieldy software engineering task, resulting in software packages that can read and process MAGE-ML from some, but not all producers. This Tower of MAGE-ML Babel bars the unencumbered exchange of microarray experiment descriptions couched in MAGE-ML. We have developed XBabelPhish - an XQuery-based technology for translating one MAGE-ML variant into another. XBabelPhish's use is not restricted to translating MAGE-ML documents. It can transform XML files independent of their DTD, XML schema, or semantic content. Moreover, it is designed to work on very large (> 200 Mb.) files, which are common in the world of MAGE-ML. XBabelPhish provides a way to inter-translate MAGE-ML variants for improved interchange of microarray experiment information. More generally, it can be used to transform most XML files, including very large ones that exceed the capacity of most XML tools.

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

Sublet, J.-Ch.; Koning, A.J.; Forrest, R.A.

The reasons for the conversion of the European Activation File, EAF into ENDF-6 format are threefold. First, it significantly enhances the JEFF-3.0 release by the addition of an activation file. Second, to considerably increase its usage by using a recognized, official file format, allowing existing plug-in processes to be effective; and third, to move towards a universal nuclear data file in contrast to the current separate general and special-purpose files. The format chosen for the JEFF-3.0/A file uses reaction cross sections (MF-3), cross sections (MF-10), and multiplicities (MF-9). Having the data in ENDF-6 format allows the ENDF suite of utilitiesmore » and checker codes to be used alongside many other utility, visualizing, and processing codes. It is based on the EAF activation file used for many applications from fission to fusion, including dosimetry, inventories, depletion-transmutation, and geophysics. JEFF-3.0/A takes advantage of four generations of EAF files. Extensive benchmarking activities on these files provide feedback and validation with integral measurements. These, in parallel with a detailed graphical analysis based on EXFOR, have been applied stimulating new measurements, significantly increasing the quality of this activation file. The next step is to include the EAF uncertainty data for all channels into JEFF-3.0/A.« less

Trick Simulation Environment 07

NASA Technical Reports Server (NTRS)

Lin, Alexander S.; Penn, John M.

2012-01-01

The Trick Simulation Environment is a generic simulation toolkit used for constructing and running simulations. This release includes a Monte Carlo analysis simulation framework and a data analysis package. It produces all auto documentation in XML. Also, the software is capable of inserting a malfunction at any point during the simulation. Trick 07 adds variable server output options and error messaging and is capable of using and manipulating wide characters for international support. Wide character strings are available as a fundamental type for variables processed by Trick. A Trick Monte Carlo simulation uses a statistically generated, or predetermined, set of inputs to iteratively drive the simulation. Also, there is a framework in place for optimization and solution finding where developers may iteratively modify the inputs per run based on some analysis of the outputs. The data analysis package is capable of reading data from external simulation packages such as MATLAB and Octave, as well as the common comma-separated values (CSV) format used by Excel, without the use of external converters. The file formats for MATLAB and Octave were obtained from their documentation sets, and Trick maintains generic file readers for each format. XML tags store the fields in the Trick header comments. For header files, XML tags for structures and enumerations, and the members within are stored in the auto documentation. For source code files, XML tags for each function and the calling arguments are stored in the auto documentation. When a simulation is built, a top level XML file, which includes all of the header and source code XML auto documentation files, is created in the simulation directory. Trick 07 provides an XML to TeX converter. The converter reads in header and source code XML documentation files and converts the data to TeX labels and tables suitable for inclusion in TeX documents. A malfunction insertion capability allows users to override the value of any simulation variable, or call a malfunction job, at any time during the simulation. Users may specify conditions, use the return value of a malfunction trigger job, or manually activate a malfunction. The malfunction action may consist of executing a block of input file statements in an action block, setting simulation variable values, call a malfunction job, or turn on/off simulation jobs.

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.

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...

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.

The GPM Common Calibrated Brightness Temperature Product

NASA Technical Reports Server (NTRS)

Stout, John; Berg, Wesley; Huffman, George; Kummerow, Chris; Stocker, Erich

2005-01-01

The Global Precipitation Measurement (GPM) project will provide a core satellite carrying the GPM Microwave Imager (GMI) and will use microwave observations from a constellation of other satellites. Each partner with a satellite in the constellation will have a calibration that meets their own requirements and will decide on the format to archive their brightness temperature (Tb) record in GPM. However, GPM multi-sensor precipitation algorithms need to input intercalibrated Tb's in order to avoid differences among sensors introducing artifacts into the longer term climate record of precipitation. The GPM Common Calibrated Brightness Temperature Product is intended to address this problem by providing intercalibrated Tb data, called "Tc" data, where the "c" stands for common. The precipitation algorithms require a Tc file format that is both generic and flexible enough to accommodate the different passive microwave instruments. The format will provide detailed information on the processing history in order to allow future researchers to have a record of what was done. The format will be simple, including the main items of scan time, latitude, longitude, and Tc. It will also provide spacecraft orientation, spacecraft location, orbit, and instrument scan type (cross-track or conical). Another simplification is to store data in real numbers, avoiding the ambiguity of scaled data. Finally, units and descriptions will be provided in the product. The format is built on the concept of a swath, which is a series of scans that have common geolocation and common scan geometry. Scan geometry includes pixels per scan, sensor orientation, scan type, and incidence angles. The Tc algorithm and data format are being tested using the pre-GPM Precipitation Processing System (PPS) software to generate formats and 1/0 routines. In the test, data from SSM/I, TMI, AMSR-E, and WindSat are being processed and written as Tc products.

Preliminary Geologic Map of the Topanga 7.5' Quadrangle, Southern California: A Digital Database

USGS Publications Warehouse

Yerkes, R.F.; Campbell, R.H.

1995-01-01

INTRODUCTION This Open-File report is a digital geologic map database. This pamphlet serves to introduce and describe the digital data. There is no paper map included in the Open-File report. This digital map database is compiled from previously published sources combined with some new mapping and modifications in nomenclature. The geologic map database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U. S. Geological Survey. For detailed descriptions of the units, their stratigraphic relations and sources of geologic mapping consult Yerkes and Campbell (1994). More specific information about the units may be available in the original sources. The content and character of the database and methods of obtaining it are described herein. The geologic map database itself, consisting of three ARC coverages and one base layer, can be obtained over the Internet or by magnetic tape copy as described below. The processes of extracting the geologic map database from the tar file, and importing the ARC export coverages (procedure described herein), will result in the creation of an ARC workspace (directory) called 'topnga.' The database was compiled using ARC/INFO version 7.0.3, a commercial Geographic Information System (Environmental Systems Research Institute, Redlands, California), with version 3.0 of the menu interface ALACARTE (Fitzgibbon and Wentworth, 1991, Fitzgibbon, 1991, Wentworth and Fitzgibbon, 1991). It is stored in uncompressed ARC export format (ARC/INFO version 7.x) in a compressed UNIX tar (tape archive) file. The tar file was compressed with gzip, and may be uncompressed with gzip, which is available free of charge via the Internet from the gzip Home Page (http://w3.teaser.fr/~jlgailly/gzip). A tar utility is required to extract the database from the tar file. This utility is included in most UNIX systems, and can be obtained free of charge via the Internet from Internet Literacy's Common Internet File Formats Webpage http://www.matisse.net/files/formats.html). ARC/INFO export files (files with the .e00 extension) can be converted into ARC/INFO coverages in ARC/INFO (see below) and can be read by some other Geographic Information Systems, such as MapInfo via ArcLink and ESRI's ArcView (version 1.0 for Windows 3.1 to 3.11 is available for free from ESRI's web site: http://www.esri.com). 1. Different base layer - The original digital database included separates clipped out of the Los Angeles 1:100,000 sheet. This release includes a vectorized scan of a scale-stable negative of the Topanga 7.5 minute quadrangle. 2. Map projection - The files in the original release were in polyconic projection. The projection used in this release is state plane, which allows for the tiling of adjacent quadrangles. 3. File compression - The files in the original release were compressed with UNIX compression. The files in this release are compressed with gzip.

Carolinas Coastal Change Processes Project data report for observations near Diamond Shoals, North Carolina, January-May 2009

USGS Publications Warehouse

Armstrong, Brandy N.; Warner, John C.; Voulgaris, George; List, Jeffrey H.; Thieler, E. Robert; Martini, Marinna A.; Montgomery, Ellyn T.

2011-01-01

This Open-File Report provides information collected for an oceanographic field study that occurred during January - May 2009 to investigate processes that control the sediment transport dynamics at Diamond Shoals, North Carolina. The objective of this report is to make the data available in digital form and to provide information to facilitate further analysis of the data. The report describes the background, experimental setup, equipment, and locations of the sensor deployments. The edited data are presented in time-series plots for rapid visualization of the data set, and in data files that are in the Network Common Data Format (netcdf). Supporting observational data are also included.

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

PubMed

Smelter, Andrey; Moseley, Hunter N B

2018-01-01

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package. This Python package, named 'mwtab', is a parser for the domain-specific 'mwTab' flat file format, which provides facilities for reading, accessing, and writing 'mwTab' formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given 'mwTab' formatted file. In order to develop the 'mwtab' package we used the official 'mwTab' format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. The 'mwtab' package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating 'mwTab' formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, 'pythonic' access and manipulation of data and metadata. Also, the package provides facilities to convert 'mwTab' files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The 'mwtab' package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between 'mwTab' and JSONized formats in raw text and a variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

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.

Data format standard for sharing light source measurements

NASA Astrophysics Data System (ADS)

Gregory, G. Groot; Ashdown, Ian; Brandenburg, Willi; Chabaud, Dominique; Dross, Oliver; Gangadhara, Sanjay; Garcia, Kevin; Gauvin, Michael; Hansen, Dirk; Haraguchi, Kei; Hasna, Günther; Jiao, Jianzhong; Kelley, Ryan; Koshel, John; Muschaweck, Julius

2013-09-01

Optical design requires accurate characterization of light sources for computer aided design (CAD) software. Various methods have been used to model sources, from accurate physical models to measurement of light output. It has become common practice for designers to include measured source data for design simulations. Typically, a measured source will contain rays which sample the output distribution of the source. The ray data must then be exported to various formats suitable for import into optical analysis or design software. Source manufacturers are also making measurements of their products and supplying CAD models along with ray data sets for designers. The increasing availability of data has been beneficial to the design community but has caused a large expansion in storage needs for the source manufacturers since each software program uses a unique format to describe the source distribution. In 2012, the Illuminating Engineering Society (IES) formed a working group to understand the data requirements for ray data and recommend a standard file format. The working group included representatives from software companies supplying the analysis and design tools, source measurement companies providing metrology, source manufacturers creating the data and users from the design community. Within one year the working group proposed a file format which was recently approved by the IES for publication as TM-25. This paper will discuss the process used to define the proposed format, highlight some of the significant decisions leading to the format and list the data to be included in the first version of the standard.

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.

Log ASCII Standard (LAS) Files for Geophysical Wireline Well Logs and Their Application to Geologic Cross Sections Through the Central Appalachian Basin

USGS Publications Warehouse

Crangle, Robert D.

2007-01-01

Introduction The U.S. Geological Survey (USGS) uses geophysical wireline well logs for a variety of purposes, including stratigraphic correlation (Hettinger, 2001, Ryder, 2002), petroleum reservoir analyses (Nelson and Bird, 2005), aquifer studies (Balch, 1988), and synthetic seismic profiles (Kulander and Ryder, 2005). Commonly, well logs are easier to visualize, manipulate, and interpret when available in a digital format. In recent geologic cross sections E-E' and D-D', constructed through the central Appalachian basin (Ryder, Swezey, and others, in press; Ryder, Crangle, and others, in press), gamma ray well log traces and lithologic logs were used to correlate key stratigraphic intervals (Fig. 1). The stratigraphy and structure of the cross sections are illustrated through the use of graphical software applications (e.g., Adobe Illustrator). The gamma ray traces were digitized in Neuralog (proprietary software) from paper well logs and converted to a Log ASCII Standard (LAS) format. Once converted, the LAS files were transformed to images through an LAS-reader application (e.g., GeoGraphix Prizm) and then overlain in positions adjacent to well locations, used for stratigraphic control, on each cross section. This report summarizes the procedures used to convert paper logs to a digital LAS format using a third-party software application, Neuralog. Included in this report are LAS files for sixteen wells used in geologic cross section E-E' (Table 1) and thirteen wells used in geologic cross section D-D' (Table 2).

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

VizieR Online Data Catalog: S4G disk galaxies stellar mass distribution (Diaz-Garcia+, 2016)

NASA Astrophysics Data System (ADS)

Diaz-Garcia, S.; Salo, H.; Laurikainen, E.

2016-08-01

We provide the tabulated radial profiles of mean stellar mass density in bins of total stellar mass (M*, from Munoz-Mateos et al., 2015ApJS..219....3M) and Hubble stage (T, from Buta et al., 2015, Cat. J/ApJS/217/32). We used the 3.6um imaging for the non-highly inclined galaxies (i<65° in Salo et al., 2015, Cat. J/ApJS/219/4) in the Spitzer Survey of Stellar Structure in Galaxies (Sheth et al., 2010, Cat. J/PASP/122/1397). We also provide the averaged stellar contribution to the circular velocity, computed from the radial force profiles of individual galaxies (from Diaz-Garcia et al., 2016A&A...587A.160D). Besides, we provide the FITS files of the bar synthetic images (2D) obtained by stacking images rescaled to a common frame determined by the bar parameters (from Herrera-Endoqui et al., 2015A&A...582A..86H) in bins of M*, T, and galaxy family (from Buta et al. 2015). For the bar stacks, we also tabulate the azimuthally averaged luminosity profiles, the tangential-to-radial forces (Qt), the m=2,4 Fourier amplitudes (A2,A4), and the radial profiles of ellipticity and b4 parameter. The fits files (.fit) of the bar stacks, in units of flux (MJy/sr). The pixel size is 0.02 x rbar, where rbar refers to the bar radius. The images are cut at a radius of 3 x rbar. In every folder, the terminology used to label the ".dat" and ".fit" files, in relation to their content, is the following: a) The term "starmass" is used when the binning of the sample was based on the total stellar mass of the galaxy, from Munoz-Mateos et al. (2015ApJS..219....3M). We indicate the common logarithm of the boundaries: (8.5,9.9.5,10,10.5,11). b) The term "ttype" is used when the binning of the sample was based on the Hubble stage of the galaxy (-3,0,3,5,8,11), from Buta et al. (2015, Cat. J/ApJS/217/32) c) The term "family" is used when the binning of the sample was based on the morphological family of the galaxy (AB,AB,AB,B), from Buta et al. (2015, Cat. J/ApJS/217/32). d) The term "hr" is used when the 1-D luminosity stacks were obtained in a common frame determined by the scalelength of the disks (from Salo et al., 2015, Cat. J/ApJS/219/4). e) The term "kpc" is used when the 1-D luminosity stacks were obtained in a common frame determined by the disk extent in physical units (kpc). f) The term "barred" is used when only barred galaxies are stacked (according to Buta et al., 2015, Cat. J/ApJS/217/32). g) The term "unbarred" is used when only non-barred galaxies are stacked. IDL reading: readcol,'luminositydiskkpc/luminositydiskkpc_*.dat',Radius,$ Steldens,bSteldens,BSteldens,SuBr,bSuBr,BSuBr,Nsample,$ format='F,F,F,F,F,F,F,F',delim=' ' readcol,'luminositydiskhr/luminositydiskhr_*.dat',Radius,$ Steldens,bSteldens,BSteldens,SuBr,bSuBr,BSuB,Nsample,$ format='F,F,F,F,F,F,F,F',delim=' ' readcol,'vrotdiskkpc/vrotdiskkpc_*.dat',Radius,Vrotmean,$ Vrotmedian,Sigma,Nsample,format='F,F,F,F,F',delim=' ' readcol,'vrotdiskhr/vrotdiskhr_*.dat',Radius,Vrotmean,Vrotmedian,$ Sigma,Nsample,format='F,F,F,F,F',delim=' ' readcol,'luminositybar/barsradialluminosity*.dat',Radius,$ Steldens,SuBr,format='F,F,F',delim=' ' readcol,'forceprofbar/barsradialforces_*.dat',Radius,Qt,A2,A4,$ format='F,F,F,F',delim=' ' readcol,'ellipseprofbar/barsradialellipse_*.dat',Radius,ellipticity,b4,$ format='F,F,F',delim=' ' fitsread,'barstackfits/barstack_*.fit',image (10 data files).

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.

Chemicals identified in feral and food animals: a data base. First annual report, October 1981. Volume I. Records 1-532

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

Cone, M.V.; Faust, R.A.; Baldauf, M.F.

This data file is a companion to Chemicals Identified in Human Biological Media, A Data Base, and follows basically the same format. The data base on human burden is in its third year of publication. This is the first annual report for the feral and food animal file. Data were obtained primarily from the open literature through manual searches (retrospective to 1979) of the journals listed in Appendix A. The data base now contains information on 60 different substances. Chemicals are listed by Chemical Abstracts Service (CAS) registry numbers and preferred names in Appendix B. For the user's convenience, cross-referencedmore » chemical lists of CAS preferred and common names are provided in Appendix C. The animals, tissues, and body fluids found to be contaminated by these chemicals are listed in Appendix D. The data base is published annually in tabular format with indices and chemical listings that allow specific searching. A limited number of custom computer searches of the data base are available in special cases when the published format does not allow for retrieval of needed information.« less

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.

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.

The Bio-Community Perl toolkit for microbial ecology.

PubMed

Angly, Florent E; Fields, Christopher J; Tyson, Gene W

2014-07-01

The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. © The Author 2014. Published by Oxford University Press.

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.

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

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.

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...

mmView: a web-based viewer of the mmCIF format

PubMed Central

2011-01-01

Background Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited. Findings In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol. Conclusions The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user's computer, and as a publicly available web server. PMID:21486459

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...

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...

26 CFR 1.1502-75 - Filing of consolidated returns.

Code of Federal Regulations, 2010 CFR

2010-04-01

... the common parent, may for good cause shown grant permission to a group to discontinue filing... extensions of time) for the filing of the common parent's return. Such consolidated return may not be... the common parent corporation establishes to the satisfaction of the Commissioner that the failure of...

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).

The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.

PubMed

Gorgolewski, Krzysztof J; Auer, Tibor; Calhoun, Vince D; Craddock, R Cameron; Das, Samir; Duff, Eugene P; Flandin, Guillaume; Ghosh, Satrajit S; Glatard, Tristan; Halchenko, Yaroslav O; Handwerker, Daniel A; Hanke, Michael; Keator, David; Li, Xiangrui; Michael, Zachary; Maumet, Camille; Nichols, B Nolan; Nichols, Thomas E; Pellman, John; Poline, Jean-Baptiste; Rokem, Ariel; Schaefer, Gunnar; Sochat, Vanessa; Triplett, William; Turner, Jessica A; Varoquaux, Gaël; Poldrack, Russell A

2016-06-21

The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard for organizing and describing MRI datasets. The BIDS standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations.

The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments

PubMed Central

Gorgolewski, Krzysztof J.; Auer, Tibor; Calhoun, Vince D.; Craddock, R. Cameron; Das, Samir; Duff, Eugene P.; Flandin, Guillaume; Ghosh, Satrajit S.; Glatard, Tristan; Halchenko, Yaroslav O.; Handwerker, Daniel A.; Hanke, Michael; Keator, David; Li, Xiangrui; Michael, Zachary; Maumet, Camille; Nichols, B. Nolan; Nichols, Thomas E.; Pellman, John; Poline, Jean-Baptiste; Rokem, Ariel; Schaefer, Gunnar; Sochat, Vanessa; Triplett, William; Turner, Jessica A.; Varoquaux, Gaël; Poldrack, Russell A.

2016-01-01

The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard for organizing and describing MRI datasets. The BIDS standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations. PMID:27326542

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.

Fifth Disease

MedlinePlus

... because it was fifth in a list of historical classifications of common skin rash illnesses in children. ... Audio/Video file Apple Quicktime file RealPlayer file Text file Zip Archive file SAS file ePub file ...

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 ( ...

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.

Creating Interactive Graphical Overlays in the Advanced Weather Interactive Processing System Using Shapefiles and DGM Files

NASA Technical Reports Server (NTRS)

Barrett, Joe H., III; Lafosse, Richard; Hood, Doris; Hoeth, Brian

2007-01-01

Graphical overlays can be created in real-time in the Advanced Weather Interactive Processing System (AWIPS) using shapefiles or Denver AWIPS Risk Reduction and Requirements Evaluation (DARE) Graphics Metafile (DGM) files. This presentation describes how to create graphical overlays on-the-fly for AWIPS, by using two examples of AWIPS applications that were created by the Applied Meteorology Unit (AMU) located at Cape Canaveral Air Force Station (CCAFS), Florida. The first example is the Anvil Threat Corridor Forecast Tool, which produces a shapefile that depicts a graphical threat corridor of the forecast movement of thunderstorm anvil clouds, based on the observed or forecast upper-level winds. This tool is used by the Spaceflight Meteorology Group (SMG) at Johnson Space Center, Texas and 45th Weather Squadron (45 WS) at CCAFS to analyze the threat of natural or space vehicle-triggered lightning over a location. The second example is a launch and landing trajectory tool that produces a DGM file that plots the ground track of space vehicles during launch or landing. The trajectory tool can be used by SMG and the 45 WS forecasters to analyze weather radar imagery along a launch or landing trajectory. The presentation will list the advantages and disadvantages of both file types for creating interactive graphical overlays in future AWIPS applications. Shapefiles are a popular format used extensively in Geographical Information Systems. They are usually used in AWIPS to depict static map backgrounds. A shapefile stores the geometry and attribute information of spatial features in a dataset (ESRI 1998). Shapefiles can contain point, line, and polygon features. Each shapefile contains a main file, index file, and a dBASE table. The main file contains a record for each spatial feature, which describes the feature with a list of its vertices. The index file contains the offset of each record from the beginning of the main file. The dBASE table contains records for each attribute. Attributes are commonly used to label spatial features. Shapefiles can be viewed, but not created in AWIPS. As a result, either third-party software can be installed on an AWIPS workstation, or new software must be written to create shapefiles in the correct format.

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...

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

The Time Series Data Server (TSDS) for Standards-Compliant, Convenient, and Efficient Access to Time Series Data

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Weigel, R. S.; Wilson, A.; Ware Dewolfe, A.

2009-12-01

Data analysis in the physical sciences is often plagued by the difficulty in acquiring the desired data. A great deal of work has been done in the area of metadata and data discovery, however, many such discoveries simply provide links that lead directly to a data file. Often these files are impractically large, containing more time samples or variables than desired, and are slow to access. Once these files are downloaded, format issues further complicate using the data. Some data servers have begun to address these problems by improving data virtualization and ease of use. However, these services often don't scale to large datasets. Also, the generic nature of the data models used by these servers, while providing greater flexibility, may complicate setting up such a service for data providers and limit sufficient semantics that would otherwise simplify use for clients, machine or human. The Time Series Data Server (TSDS) aims to address these problems within the limited, yet common, domain of time series data. With the simplifying assumption that all data products served are a function of time, the server can optimize for data access based on time subsets, a common use case. The server also supports requests for specific variables, which can be of type scalar, structure, or sequence. It also supports data types with higher level semantics, such as "spectrum." The TSDS is implemented using Java Servlet technology and can be dropped into any servlet container and customized for a data provider's needs. The interface is based on OPeNDAP (http://opendap.org) and conforms to the Data Acces Protocol (DAP) 2.0, a NASA standard (ESDS-RFC-004), which defines a simple HTTP request and response paradigm. Thus a TSDS server instance is a compliant OPeNDAP server that can be accessed by any OPeNDAP client or directly via RESTful web service requests. The TSDS reads the data that it serves into a common data model via the NetCDF Markup Language (NcML, http://www.unidata.ucar.edu/software/netcdf/ncml/) which enables dataset virtualization. An NcML file can expose a single file, a subset, or an aggregation of files as a single, logical dataset. With the appropriate NcML adapter, the TSDS can read data from its native format, eliminating the need for data providers to reformat their data and lowering the barrier for integration. Data can even be read via remote services which is important for enabling VxOs to be truly virtual. The TSDS provides reading, writing, and filtering capabilities through a modular framework. A collection of standard modules is available and customized modules are easy to create and integrate. This way the TSDS can read and write data in a variety of formats and apply filters to them an a manner customizable to meet the needs of both the data providers and consumers. The TSDS server is currently in use serving solar irradiance data from the LASP Interactive Solar IRradiance Datacenter (LISIRD, http://lasp.colorado.edu/lisird/), and is being introduced into the space physics virtual observatory community. The TSDS software is Open Source and available at SourceForge.

Integrating SAS and GIS software to improve habitat-use estimates from radiotelemetry data

USGS Publications Warehouse

Kenow, K.P.; Wright, R.G.; Samuel, M.D.; Rasmussen, P.W.

2001-01-01

Radiotelemetry has been used commonly to remotely determine habitat use by a variety of wildlife species. However, habitat misclassification can occur because the true location of a radiomarked animal can only be estimated. Analytical methods that provide improved estimates of habitat use from radiotelemetry location data using a subsampling approach have been proposed previously. We developed software, based on these methods, to conduct improved habitat-use analyses. A Statistical Analysis System (SAS)-executable file generates a random subsample of points from the error distribution of an estimated animal location and formats the output into ARC/INFO-compatible coordinate and attribute files. An associated ARC/INFO Arc Macro Language (AML) creates a coverage of the random points, determines the habitat type at each random point from an existing habitat coverage, sums the number of subsample points by habitat type for each location, and outputs tile results in ASCII format. The proportion and precision of habitat types used is calculated from the subsample of points generated for each radiotelemetry location. We illustrate the method and software by analysis of radiotelemetry data for a female wild turkey (Meleagris gallopavo).

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.

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...

KungFQ: a simple and powerful approach to compress fastq files.

PubMed

Grassi, Elena; Di Gregorio, Federico; Molineris, Ivan

2012-01-01

Nowadays storing data derived from deep sequencing experiments has become pivotal and standard compression algorithms do not exploit in a satisfying manner their structure. A number of reference-based compression algorithms have been developed but they are less adequate when approaching new species without fully sequenced genomes or nongenomic data. We developed a tool that takes advantages of fastq characteristics and encodes them in a binary format optimized in order to be further compressed with standard tools (such as gzip or lzma). The algorithm is straightforward and does not need any external reference file, it scans the fastq only once and has a constant memory requirement. Moreover, we added the possibility to perform lossy compression, losing some of the original information (IDs and/or qualities) but resulting in smaller files; it is also possible to define a quality cutoff under which corresponding base calls are converted to N. We achieve 2.82 to 7.77 compression ratios on various fastq files without losing information and 5.37 to 8.77 losing IDs, which are often not used in common analysis pipelines. In this paper, we compare the algorithm performance with known tools, usually obtaining higher compression levels.

A JPEG backward-compatible HDR image compression

NASA Astrophysics Data System (ADS)

Korshunov, Pavel; Ebrahimi, Touradj

2012-10-01

High Dynamic Range (HDR) imaging is expected to become one of the technologies that could shape next generation of consumer digital photography. Manufacturers are rolling out cameras and displays capable of capturing and rendering HDR images. The popularity and full public adoption of HDR content is however hindered by the lack of standards in evaluation of quality, file formats, and compression, as well as large legacy base of Low Dynamic Range (LDR) displays that are unable to render HDR. To facilitate wide spread of HDR usage, the backward compatibility of HDR technology with commonly used legacy image storage, rendering, and compression is necessary. Although many tone-mapping algorithms were developed for generating viewable LDR images from HDR content, there is no consensus on which algorithm to use and under which conditions. This paper, via a series of subjective evaluations, demonstrates the dependency of perceived quality of the tone-mapped LDR images on environmental parameters and image content. Based on the results of subjective tests, it proposes to extend JPEG file format, as the most popular image format, in a backward compatible manner to also deal with HDR pictures. To this end, the paper provides an architecture to achieve such backward compatibility with JPEG and demonstrates efficiency of a simple implementation of this framework when compared to the state of the art HDR image compression.

Radio data archiving system

NASA Astrophysics Data System (ADS)

Knapic, C.; Zanichelli, A.; Dovgan, E.; Nanni, M.; Stagni, M.; Righini, S.; Sponza, M.; Bedosti, F.; Orlati, A.; Smareglia, R.

2016-07-01

Radio Astronomical Data models are becoming very complex since the huge possible range of instrumental configurations available with the modern Radio Telescopes. What in the past was the last frontiers of data formats in terms of efficiency and flexibility is now evolving with new strategies and methodologies enabling the persistence of a very complex, hierarchical and multi-purpose information. Such an evolution of data models and data formats require new data archiving techniques in order to guarantee data preservation following the directives of Open Archival Information System and the International Virtual Observatory Alliance for data sharing and publication. Currently, various formats (FITS, MBFITS, VLBI's XML description files and ancillary files) of data acquired with the Medicina and Noto Radio Telescopes can be stored and handled by a common Radio Archive, that is planned to be released to the (inter)national community by the end of 2016. This state-of-the-art archiving system for radio astronomical data aims at delegating as much as possible to the software setting how and where the descriptors (metadata) are saved, while the users perform user-friendly queries translated by the web interface into complex interrogations on the database to retrieve data. In such a way, the Archive is ready to be Virtual Observatory compliant and as much as possible user-friendly.

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

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...

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.

Using the Auditory Hazard Assessment Algorithm for Humans (AHAAH) Software, Beta Release W93e

DTIC Science & Technology

2009-09-01

Hazard Assessment Algorithm for Humans (AHAAH) Does The AHAAH is an electro- acoustic model of the ear used to evaluate the hazard of impulse sounds...format is commonly used for recording music ; thus, these are typically stereo files and contain a “right” and a “left” channel as well as a header... acoustic data (sometimes deliberately induced in recording to maximize the digitizer’s dynamic range), it must be removed. When Set Baseline is

CBEFF Common Biometric Exchange File Format

DTIC Science & Technology

2001-01-03

and systems. Points of contact for CBEFF and liaisons to other organizations can be found in Appendix F. 2. Purpose The purpose of CBEFF is...0x40 Signature Dynamics 0x80 Keystroke Dynamics 0x100 Lip Movement 0x200 Thermal Face Image 0x400 Thermal Hand Image 0x800 Gait 0x1000 Body...this process is negligible from the Biometric Objects point of view, unless the process creating the livescan sample to compare against the

Text Exchange System

NASA Technical Reports Server (NTRS)

Snyder, W. V.; Hanson, R. J.

1986-01-01

Text Exchange System (TES) exchanges and maintains organized textual information including source code, documentation, data, and listings. System consists of two computer programs and definition of format for information storage. Comprehensive program used to create, read, and maintain TES files. TES developed to meet three goals: First, easy and efficient exchange of programs and other textual data between similar and dissimilar computer systems via magnetic tape. Second, provide transportable management system for textual information. Third, provide common user interface, over wide variety of computing systems, for all activities associated with text exchange.

[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.

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.

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.

The NetLogger Toolkit V2.0

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

Gunter, Dan; Lee, Jason; Stoufer, Martin

2003-03-28

The NetLogger Toolkit is designed to monitor, under actual operating conditions, the behavior of all the elements of the application-to-application communication path in order to determine exactly where time is spent within a complex system Using NetLogger, distnbuted application components are modified to produce timestamped logs of "interesting" events at all the critical points of the distributed system Events from each component are correlated, which allov^ one to characterize the performance of all aspects of the system and network in detail. The NetLogger Toolkit itself consists of four components an API and library of functions to simplify the generation ofmore » application-level event logs, a set of tools for collecting and sorting log files, an event archive system, and a tool for visualization and analysis of the log files In order to instrument an application to produce event logs, the application developer inserts calls to the NetLogger API at all the critical points in the code, then links the application with the NetLogger library All the tools in the NetLogger Toolkit share a common log format, and assume the existence of accurate and synchronized system clocks NetLogger messages can be logged using an easy-to-read text based format based on the lETF-proposed ULM format, or a binary format that can still be used through the same API but that is several times faster and smaller, with performance comparable or better than binary message formats such as MPI, XDR, SDDF-Binary, and PBIO. The NetLogger binary format is both highly efficient and self-describing, thus optimized for the dynamic message construction and parsing of application instrumentation. NetLogger includes an "activation" API that allows NetLogger logging to be turned on, off, or modified by changing an external file This IS useful for activating logging in daemons/services (e g GndFTP server). The NetLogger reliability API provides the ability to specify backup logging locations and penodically try to reconnect broken TCP pipe. A typical use for this is to store data on local disk while net is down. An event archiver can log one or more incoming NetLogger streams to a local disk file (netlogd) or to a mySQL database (netarchd). We have found exploratory, visual analysis of the log event data to be the most useful means of determining the causes of performance anomalies The NetLogger Visualization tool, niv, has been developed to provide a flexible and interactive graphical representation of system-level and application-level events.« less

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...

Configuration Management File Manager Developed for Numerical Propulsion System Simulation

NASA Technical Reports Server (NTRS)

Follen, Gregory J.

1997-01-01

One of the objectives of the High Performance Computing and Communication Project's (HPCCP) Numerical Propulsion System Simulation (NPSS) is to provide a common and consistent way to manage applications, data, and engine simulations. The NPSS Configuration Management (CM) File Manager integrated with the Common Desktop Environment (CDE) window management system provides a common look and feel for the configuration management of data, applications, and engine simulations for U.S. engine companies. In addition, CM File Manager provides tools to manage a simulation. Features include managing input files, output files, textual notes, and any other material normally associated with simulation. The CM File Manager includes a generic configuration management Application Program Interface (API) that can be adapted for the configuration management repositories of any U.S. engine company.

LIBMAKER

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

2015-08-01

Version 00 COG LibMaker contains various utilities to convert common data formats into a format usable by the COG - Multi-particle Monte Carlo Code System package, (C00777MNYCP01). Utilities included: ACEtoCOG - ACE formatted neutron data: Currently ENDFB7R0.BNL, ENDFB7R1.BNL, JEFF3.1, JEFF3.1.1, JEFF3.1.2, MCNP.50c, MCNP.51c, MCNP.55c, MCNP.66c, and MCNP.70c. ACEUtoCOG - ACEU formatted photonuclear data: Currently PN.MCNP.30c and PN.MCNP.70u. ACTLtoCOG - Creates a COG library from ENDL formatted activation data COG library. EDDLtoCOG - Creates a COG library from ENDL formatted LLNL deuteron data. ENDLtoCOG - Creates a COG library from ENDL formatted LLNL neutron data. EPDLtoCOG - Creates a COG librarymore » from ENDL formatted LLNL photon data. LEX - Creates a COG dictionary file. SAB.ACEtoCOG - Creates a COG library from ACE formatted S(a,b) data. SABtoCOG - Creates a COG library from ENDF6 formatted S(a,b) data. URRtoCOG - Creates a COG library from ACE formatted probability table data. This package also includes library checking and bit swapping capability.« less

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

Advances in a distributed approach for ocean model data interoperability

USGS Publications Warehouse

Signell, Richard P.; Snowden, Derrick P.

2014-01-01

An infrastructure for earth science data is emerging across the globe based on common data models and web services. As we evolve from custom file formats and web sites to standards-based web services and tools, data is becoming easier to distribute, find and retrieve, leaving more time for science. We describe recent advances that make it easier for ocean model providers to share their data, and for users to search, access, analyze and visualize ocean data using MATLAB® and Python®. These include a technique for modelers to create aggregated, Climate and Forecast (CF) metadata convention datasets from collections of non-standard Network Common Data Form (NetCDF) output files, the capability to remotely access data from CF-1.6-compliant NetCDF files using the Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), a metadata standard for unstructured grid model output (UGRID), and tools that utilize both CF and UGRID standards to allow interoperable data search, browse and access. We use examples from the U.S. Integrated Ocean Observing System (IOOS®) Coastal and Ocean Modeling Testbed, a project in which modelers using both structured and unstructured grid model output needed to share their results, to compare their results with other models, and to compare models with observed data. The same techniques used here for ocean modeling output can be applied to atmospheric and climate model output, remote sensing data, digital terrain and bathymetric data.

Gro2mat: a package to efficiently read gromacs output in MATLAB.

PubMed

Dien, Hung; Deane, Charlotte M; Knapp, Bernhard

2014-07-30

Molecular dynamics (MD) simulations are a state-of-the-art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc-format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc. Copyright © 2014 Wiley Periodicals, Inc.

Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and PIONE with Eos.

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

Eos (Extensible object-oriented system) is one of the powerful applications for image processing of electron micrographs. In usual cases, Eos works with only character user interfaces (CUI) under the operating systems (OS) such as OS-X or Linux, not user-friendly. Thus, users of Eos need to be expert at image processing of electron micrographs, and have a little knowledge of computer science, as well. However, all the persons who require Eos does not an expert for CUI. Thus we extended Eos to a web system independent of OS with graphical user interfaces (GUI) by integrating web browser.Advantage to use web browser is not only to extend Eos with GUI, but also extend Eos to work under distributed computational environment. Using Ajax (Asynchronous JavaScript and XML) technology, we implemented more comfortable user-interface on web browser. Eos has more than 400 commands related to image processing for electron microscopy, and the usage of each command is different from each other. Since the beginning of development, Eos has managed their user-interface by using the interface definition file of "OptionControlFile" written in CSV (Comma-Separated Value) format, i.e., Each command has "OptionControlFile", which notes information for interface and its usage generation. Developed GUI system called "Zephyr" (Zone for Easy Processing of HYpermedia Resources) also accessed "OptionControlFIle" and produced a web user-interface automatically, because its mechanism is mature and convenient,The basic actions of client side system was implemented properly and can supply auto-generation of web-form, which has functions of execution, image preview, file-uploading to a web server. Thus the system can execute Eos commands with unique options for each commands, and process image analysis. There remain problems of image file format for visualization and workspace for analysis: The image file format information is useful to check whether the input/output file is correct and we also need to provide common workspace for analysis because the client is physically separated from a server. We solved the file format problem by extension of rules of OptionControlFile of Eos. Furthermore, to solve workspace problems, we have developed two type of system. The first system is to use only local environments. The user runs a web server provided by Eos, access to a web client through a web browser, and manipulate the local files with GUI on the web browser. The second system is employing PIONE (Process-rule for Input/Output Negotiation Environment), which is our developing platform that works under heterogenic distributed environment. The users can put their resources, such as microscopic images, text files and so on, into the server-side environment supported by PIONE, and so experts can write PIONE rule definition, which defines a workflow of image processing. PIONE run each image processing on suitable computers, following the defined rule. PIONE has the ability of interactive manipulation, and user is able to try a command with various setting values. In this situation, we contribute to auto-generation of GUI for a PIONE workflow.As advanced functions, we have developed a module to log user actions. The logs include information such as setting values in image processing, procedure of commands and so on. If we use the logs effectively, we can get a lot of advantages. For example, when an expert may discover some know-how of image processing, other users can also share logs including his know-hows and so we may obtain recommendation workflow of image analysis, if we analyze logs. To implement social platform of image processing for electron microscopists, we have developed system infrastructure, as well. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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).

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.

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.

A New Archive of UKIRT Legacy Data at CADC

NASA Astrophysics Data System (ADS)

Bell, G. S.; Currie, M. J.; Redman, R. O.; Purves, M.; Jenness, T.

2014-05-01

We describe a new archive of legacy data from the United Kingdom Infrared Telescope (UKIRT) at the Canadian Astronomy Data Centre (CADC) containing all available data from the Cassegrain instruments. The desire was to archive the raw data in as close to the original format as possible, so where the data followed our current convention of having a single data file per observation, it was archived without alteration, except for minor fixes to headers of data in FITS format to allow it to pass fitsverify and be accepted by CADC. Some of the older data comprised multiple integrations in separate files per observation, stored in either Starlink NDF or Figaro DST format. These were placed inside HDS container files, and DST files were rearranged into NDF format. The describing the observations is ingested into the CAOM-2 repository via an intermediate MongoDB header database, which will also be used to guide the ORAC-DR pipeline in generating reduced data products.

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.

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.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

VizieR Online Data Catalog: Bessel (1825) calculation for geodesic measurements (Karney+, 2010)

NASA Astrophysics Data System (ADS)

Karney, C. F. F.; Deakin, R. E.

2010-06-01

The solution of the geodesic problem for an oblate ellipsoid is developed in terms of series. Tables are provided to simplify the computation. Included here are the tables that accompanied Bessel's paper (with corrections). The tables were crafted by Bessel to be minimize the labor of hand calculations. To this end, he adjusted the intervals in the tables, the number of terms included in the series, and the number of significant digits given so that the final results are accurate to about 8 places. For that reason, the most useful form of the tables is as the PDF file which provides the tables in a layout close to the original. Also provided is the LaTeX source file for the PDF file. Finally, the data has been put into a format so that it can be read easily by computer programs. All the logarithms are in base 10 (common logarithms). The characteristic and the mantissa should be read separately (indicated as x.c and x.m in the file description). Thus the first entry in the table, -4.4, should be parsed as "-4" (the characteristic) and ".4" (the mantissa); the anti-log for this entry is 10(-4+0.4)=2.5e-4. The "Delta" columns give the first difference of the preceding column, i.e., the difference of the preceding column in the next row and the preceding column in the current row. In the printed tables these are expressed as "units in the last place" and the differences are of the rounded representations in the preceding columns (to minimize interpolation errors). In table1.dat these are given scaled to a match the format used for the preceding column, as indicated by the units given for these columns. The unit log(") (in the description within square brackets [arcsec]) means the logarithm of a quantity expressed in arcseconds. (3 data files).

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...

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.

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...

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

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 ( ...

Deep PDF parsing to extract features for detecting embedded malware.

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

Munson, Miles Arthur; Cross, Jesse S.

2011-09-01

The number of PDF files with embedded malicious code has risen significantly in the past few years. This is due to the portability of the file format, the ways Adobe Reader recovers from corrupt PDF files, the addition of many multimedia and scripting extensions to the file format, and many format properties the malware author may use to disguise the presence of malware. Current research focuses on executable, MS Office, and HTML formats. In this paper, several features and properties of PDF Files are identified. Features are extracted using an instrumented open source PDF viewer. The feature descriptions of benignmore » and malicious PDFs can be used to construct a machine learning model for detecting possible malware in future PDF files. The detection rate of PDF malware by current antivirus software is very low. A PDF file is easy to edit and manipulate because it is a text format, providing a low barrier to malware authors. Analyzing PDF files for malware is nonetheless difficult because of (a) the complexity of the formatting language, (b) the parsing idiosyncrasies in Adobe Reader, and (c) undocumented correction techniques employed in Adobe Reader. In May 2011, Esparza demonstrated that PDF malware could be hidden from 42 of 43 antivirus packages by combining multiple obfuscation techniques [4]. One reason current antivirus software fails is the ease of varying byte sequences in PDF malware, thereby rendering conventional signature-based virus detection useless. The compression and encryption functions produce sequences of bytes that are each functions of multiple input bytes. As a result, padding the malware payload with some whitespace before compression/encryption can change many of the bytes in the final payload. In this study we analyzed a corpus of 2591 benign and 87 malicious PDF files. While this corpus is admittedly small, it allowed us to test a system for collecting indicators of embedded PDF malware. We will call these indicators features throughout the rest of this report. The features are extracted using an instrumented PDF viewer, and are the inputs to a prediction model that scores the likelihood of a PDF file containing malware. The prediction model is constructed from a sample of labeled data by a machine learning algorithm (specifically, decision tree ensemble learning). Preliminary experiments show that the model is able to detect half of the PDF malware in the corpus with zero false alarms. We conclude the report with suggestions for extending this work to detect a greater variety of PDF malware.« less

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

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

A Customizable Importer for the Clinical Data Warehouses PaDaWaN and I2B2.

PubMed

Fette, Georg; Kaspar, Mathias; Dietrich, Georg; Ertl, Maximilian; Krebs, Jonathan; Stoerk, Stefan; Puppe, Frank

2017-01-01

In recent years, clinical data warehouses (CDW) storing routine patient data have become more and more popular to support scientific work in the medical domain. Although CDW systems provide interfaces to import new data, these interfaces have to be used by processing tools that are often not included in the systems themselves. In order to establish an extraction-transformation-load (ETL) workflow, already existing components have to be taken or new components have to be developed to perform the load part of the ETL. We present a customizable importer for the two CDW systems PaDaWaN and I2B2, which is able to import the most common import formats (plain text, CSV and XML files). In order to be run, the importer only needs a configuration file with the user credentials for the target CDW and a list of XML import configuration files, which determine how already exported data is indented to be imported. The importer is provided as a Java program, which has no further software requirements.

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.

Using Interactive 3D PDF for Exploring Complex Biomedical Data: Experiences and Solutions.

PubMed

Newe, Axel; Becker, Linda

2016-01-01

The Portable Document Format (PDF) is the most commonly used file format for the exchange of electronic documents. A lesser-known feature of PDF is the possibility to embed three-dimensional models and to display these models interactively with a qualified reader. This technology is well suited to present, to explore and to communicate complex biomedical data. This applies in particular for data which would suffer from a loss of information if it was reduced to a static two-dimensional projection. In this article, we present applications of 3D PDF for selected scholarly and clinical use cases in the biomedical domain. Furthermore, we present a sophisticated tool for the generation of respective PDF documents.

Pathology data integration with eXtensible Markup Language.

PubMed

Berman, Jules J

2005-02-01

It is impossible to overstate the importance of XML (eXtensible Markup Language) as a data organization tool. With XML, pathologists can annotate all of their data (clinical and anatomic) in a format that can transform every pathology report into a database, without compromising narrative structure. The purpose of this manuscript is to provide an overview of XML for pathologists. Examples will demonstrate how pathologists can use XML to annotate individual data elements and to structure reports in a common format that can be merged with other XML files or queried using standard XML tools. This manuscript gives pathologists a glimpse into how XML allows pathology data to be linked to other types of biomedical data and reduces our dependence on centralized proprietary databases.

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

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.

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.

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.

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. Kent; Greene, Emily A.; Pence, William

1993-05-01

FTOOLS, a highly modular collection of utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Research Archive Center) at NASA's Goddard Space Flight Center. Each utility performs a single simple task such as presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual utilities can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. The collection of utilities provides both generic processing and analysis utilities and utilities common to high energy astrophysics data sets. The FTOOLS software package is designed to be both compatible with IRAF and completely stand alone in a UNIX or VMS environment. The user interface is controlled by standard IRAF parameter files. The package is self documenting through the IRAF help facility and a stand alone help task. Software is written in ANSI C and FORTRAN to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

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.

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Multibody dynamics model building using graphical interfaces

NASA Technical Reports Server (NTRS)

Macala, Glenn A.

1989-01-01

In recent years, the extremely laborious task of manually deriving equations of motion for the simulation of multibody spacecraft dynamics has largely been eliminated. Instead, the dynamicist now works with commonly available general purpose dynamics simulation programs which generate the equations of motion either explicitly or implicitly via computer codes. The user interface to these programs has predominantly been via input data files, each with its own required format and peculiarities, causing errors and frustrations during program setup. Recent progress in a more natural method of data input for dynamics programs: the graphical interface, is described.

dada - a web-based 2D detector analysis tool

NASA Astrophysics Data System (ADS)

Osterhoff, Markus

2017-06-01

The data daemon, dada, is a server backend for unified access to 2D pixel detector image data stored with different detectors, file formats and saved with varying naming conventions and folder structures across instruments. Furthermore, dada implements basic pre-processing and analysis routines from pixel binning over azimuthal integration to raster scan processing. Common user interactions with dada are by a web frontend, but all parameters for an analysis are encoded into a Uniform Resource Identifier (URI) which can also be written by hand or scripts for batch processing.

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.

The ERG Science Center

NASA Astrophysics Data System (ADS)

Miyoshi, Yoshizumi; Hori, Tomoaki; Shoji, Masafumi; Teramoto, Mariko; Chang, T. F.; Segawa, Tomonori; Umemura, Norio; Matsuda, Shoya; Kurita, Satoshi; Keika, Kunihiro; Miyashita, Yukinaga; Seki, Kanako; Tanaka, Yoshimasa; Nishitani, Nozomu; Kasahara, Satoshi; Yokota, Shoichiro; Matsuoka, Ayako; Kasahara, Yoshiya; Asamura, Kazushi; Takashima, Takeshi; Shinohara, Iku

2018-06-01

The Exploration of energization and Radiation in Geospace (ERG) Science Center serves as a hub of the ERG project, providing data files in a common format and developing the space physics environment data analysis software and plug-ins for data analysis. The Science Center also develops observation plans for the ERG (Arase) satellite according to the science strategy of the project. Conjugate observations with other satellites and ground-based observations are also planned. These tasks contribute to the ERG project by achieving quick analysis and well-organized conjugate ERG satellite and ground-based observations.

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.

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).

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.

Integrated geometry and grid generation system for complex configurations

NASA Technical Reports Server (NTRS)

Akdag, Vedat; Wulf, Armin

1992-01-01

A grid generation system was developed that enables grid generation for complex configurations. The system called ICEM/CFD is described and its role in computational fluid dynamics (CFD) applications is presented. The capabilities of the system include full computer aided design (CAD), grid generation on the actual CAD geometry definition using robust surface projection algorithms, interfacing easily with known CAD packages through common file formats for geometry transfer, grid quality evaluation of the volume grid, coupling boundary condition set-up for block faces with grid topology generation, multi-block grid generation with or without point continuity and block to block interface requirement, and generating grid files directly compatible with known flow solvers. The interactive and integrated approach to the problem of computational grid generation not only substantially reduces manpower time but also increases the flexibility of later grid modifications and enhancements which is required in an environment where CFD is integrated into a product design cycle.

XenoSite server: a web-available site of metabolism prediction tool.

PubMed

Matlock, Matthew K; Hughes, Tyler B; Swamidass, S Joshua

2015-04-01

Cytochrome P450 enzymes (P450s) are metabolic enzymes that process the majority of FDA-approved, small-molecule drugs. Understanding how these enzymes modify molecule structure is key to the development of safe, effective drugs. XenoSite server is an online implementation of the XenoSite, a recently published computational model for P450 metabolism. XenoSite predicts which atomic sites of a molecule--sites of metabolism (SOMs)--are modified by P450s. XenoSite server accepts input in common chemical file formats including SDF and SMILES and provides tools for visualizing the likelihood that each atomic site is a site of metabolism for a variety of important P450s, as well as a flat file download of SOM predictions. XenoSite server is available at http://swami.wustl.edu/xenosite. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Map Database for Surficial Materials in the Conterminous United States

USGS Publications Warehouse

Soller, David R.; Reheis, Marith C.; Garrity, Christopher P.; Van Sistine, D. R.

2009-01-01

The Earth's bedrock is overlain in many places by a loosely compacted and mostly unconsolidated blanket of sediments in which soils commonly are developed. These sediments generally were eroded from underlying rock, and then were transported and deposited. In places, they exceed 1000 ft (330 m) in thickness. Where the sediment blanket is absent, bedrock is either exposed or has been weathered to produce a residual soil. For the conterminous United States, a map by Soller and Reheis (2004, scale 1:5,000,000; http://pubs.usgs.gov/of/2003/of03-275/) shows these sediments and the weathered, residual material; for ease of discussion, these are referred to as 'surficial materials'. That map was produced as a PDF file, from an Adobe Illustrator-formatted version of the provisional GIS database. The provisional GIS files were further processed without modifying the content of the published map, and are here published.

A Study of NetCDF as an Approach for High Performance Medical Image Storage

NASA Astrophysics Data System (ADS)

Magnus, Marcone; Coelho Prado, Thiago; von Wangenhein, Aldo; de Macedo, Douglas D. J.; Dantas, M. A. R.

2012-02-01

The spread of telemedicine systems increases every day. The systems and PACS based on DICOM images has become common. This rise reflects the need to develop new storage systems, more efficient and with lower computational costs. With this in mind, this article discusses a study for application in NetCDF data format as the basic platform for storage of DICOM images. The study case comparison adopts an ordinary database, the HDF5 and the NetCDF to storage the medical images. Empirical results, using a real set of images, indicate that the time to retrieve images from the NetCDF for large scale images has a higher latency compared to the other two methods. In addition, the latency is proportional to the file size, which represents a drawback to a telemedicine system that is characterized by a large amount of large image files.

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

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).

Using the K-25 C TD Common File System: A guide to CFSI (CFS Interface)

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

Not Available

1989-12-01

A CFS (Common File System) is a large, centralized file management and storage facility based on software developed at Los Alamos National Laboratory. This manual is a guide to use of the CFS available to users of the Cray UNICOS system at Martin Marietta Energy Systems, Inc., in Oak Ridge, Tennessee.

47 CFR 61.14 - Method of filing publications.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Method of filing publications. 61.14 Section 61.14 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) TARIFFS Rules for Electronic Filing § 61.14 Method of filing publications. (a) Publications filed...

ADST, Version Description Document for the BDS-D M1 1.0.0

DTIC Science & Technology

1992-12-22

1.1 date: 1992/10/01 23:32:59; author: crn-adst; state: Exp; Initial Version RCS file: ./common/include/cig- f /RCS/if...eh~eff.h,v Working file: if...libsrc/libfifo/RCS/ f -enqueue.c,v working file: f_enqueue.c head: 1.1 description: ITO - 6.6.1 baseline revision 1.1 date: 1992/10/01 23:43:13; author...crn-adst; state: Exp; Initial Version RCS file: ./common/libsrc/libfifo/RCS/ f -init.c,v working file: f -init.c head: 1.1 description: ITO - 6.6.1

Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

PubMed

Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S; Mabuchi, Hideo; Wiggins, Chris H; Gonzalez, Ruben L; Herschlag, Daniel

2015-01-16

Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

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

Lehe, Remi

Many simulation software produce data in the form of a set of field values or of a set of particle positions. (one such example is that of particle-in-cell codes, which produce data on the electromagnetic fields that they simulate.) However, each particular software uses its own particular format and layout, for the output data. This makes it difficult to compare the results of different simulation software, or to have a common visualization tool for these results. However, a standardized layout for fields and particles has recently been developed: the openPMD format ( HYPERLINK "http://www.openpmd.org/"www.openpmd.org) This format is open- source, andmore » specifies a standard way in which field data and particle data should be written. The openPMD format is already implemented in the particle-in-cell code Warp (developed at LBL) and in PIConGPU (developed at HZDR, Germany). In this context, the proposed software (openPMD-viewer) is a Python package, which allows to access and visualize any data which has been formatted according to the openPMD standard. This package contains two main components: - a Python API, which allows to read and extract the data from a openPMD file, so as to be able to work with it within the Python environment. (e.g. plot the data and reprocess it with particular Python functions) - a graphical interface, which works with the ipython notebook, and allows to quickly visualize the data and browse through a set of openPMD files. The proposed software will be typically used when analyzing the results of numerical simulations. It will be useful to quickly extract scientific meaning from a set of numerical data.« less

SGRAPH (SeismoGRAPHer): Seismic waveform analysis and integrated tools in seismology

NASA Astrophysics Data System (ADS)

Abdelwahed, Mohamed F.

2012-03-01

Although numerous seismological programs are currently available, most of them suffer from the inability to manipulate different data formats and the lack of embedded seismological tools. SeismoGRAPHer, or simply SGRAPH, is a new system for maintaining and analyzing seismic waveform data in a stand-alone, Windows-based application that manipulates a wide range of data formats. SGRAPH was intended to be a tool sufficient for performing basic waveform analysis and solving advanced seismological problems. The graphical user interface (GUI) utilities and the Windows functionalities, such as dialog boxes, menus, and toolbars, simplify the user interaction with the data. SGRAPH supports common data formats, such as SAC, SEED, GSE, ASCII, and Nanometrics Y-format, and provides the ability to solve many seismological problems with built-in inversion tools. Loaded traces are maintained, processed, plotted, and saved as SAC, ASCII, or PS (post script) file formats. SGRAPH includes Generalized Ray Theory (GRT), genetic algorithm (GA), least-square fitting, auto-picking, fast Fourier transforms (FFT), and many additional tools. This program provides rapid estimation of earthquake source parameters, location, attenuation, and focal mechanisms. Advanced waveform modeling techniques are provided for crustal structure and focal mechanism estimation. SGRAPH has been employed in the Egyptian National Seismic Network (ENSN) as a tool assisting with routine work and data analysis. More than 30 users have been using previous versions of SGRAPH in their research for more than 3 years. The main features of this application are ease of use, speed, small disk space requirements, and the absence of third-party developed components. Because of its architectural structure, SGRAPH can be interfaced with newly developed methods or applications in seismology. A complete setup file, including the SGRAPH package with the online user guide, is available.

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.

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...

The Iranian National Geodata Revision Strategy and Realization Based on Geodatabase

NASA Astrophysics Data System (ADS)

Haeri, M.; Fasihi, A.; Ayazi, S. M.

2012-07-01

In recent years, using of spatial database for storing and managing spatial data has become a hot topic in the field of GIS. Accordingly National Cartographic Center of Iran (NCC) produces - from time to time - some spatial data which is usually included in some databases. One of the NCC major projects was designing National Topographic Database (NTDB). NCC decided to create National Topographic Database of the entire country-based on 1:25000 coverage maps. The standard of NTDB was published in 1994 and its database was created at the same time. In NTDB geometric data was stored in MicroStation design format (DGN) which each feature has a link to its attribute data (stored in Microsoft Access file). Also NTDB file was produced in a sheet-wise mode and then stored in a file-based style. Besides map compilation, revision of existing maps has already been started. Key problems of NCC are revision strategy, NTDB file-based style storage and operator challenges (NCC operators are almost preferred to edit and revise geometry data in CAD environments). A GeoDatabase solution for national Geodata, based on NTDB map files and operators' revision preferences, is introduced and released herein. The proposed solution extends the traditional methods to have a seamless spatial database which it can be revised in CAD and GIS environment, simultaneously. The proposed system is the common data framework to create a central data repository for spatial data storage and management.

Interactive publications: creation and usage

NASA Astrophysics Data System (ADS)

Thoma, George R.; Ford, Glenn; Chung, Michael; Vasudevan, Kirankumar; Antani, Sameer

2006-02-01

As envisioned here, an "interactive publication" has similarities to multimedia documents that have been in existence for a decade or more, but possesses specific differentiating characteristics. In common usage, the latter refers to online entities that, in addition to text, consist of files of images and video clips residing separately in databases, rarely providing immediate context to the document text. While an interactive publication has many media objects as does the "traditional" multimedia document, it is a self-contained document, either as a single file with media files embedded within it, or as a "folder" containing tightly linked media files. The main characteristic that differentiates an interactive publication from a traditional multimedia document is that the reader would be able to reuse the media content for analysis and presentation, and to check the underlying data and possibly derive alternative conclusions leading, for example, to more in-depth peer reviews. We have created prototype publications containing paginated text and several media types encountered in the biomedical literature: 3D animations of anatomic structures; graphs, charts and tabular data; cell development images (video sequences); and clinical images such as CT, MRI and ultrasound in the DICOM format. This paper presents developments to date including: a tool to convert static tables or graphs into interactive entities, authoring procedures followed to create prototypes, and advantages and drawbacks of each of these platforms. It also outlines future work including meeting the challenge of network distribution for these large files.

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.

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.

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).

How strong are passwords used to protect personal health information in clinical trials?

PubMed

El Emam, Khaled; Moreau, Katherine; Jonker, Elizabeth

2011-02-11

Findings and statements about how securely personal health information is managed in clinical research are mixed. The objective of our study was to evaluate the security of practices used to transfer and share sensitive files in clinical trials. Two studies were performed. First, 15 password-protected files that were transmitted by email during regulated Canadian clinical trials were obtained. Commercial password recovery tools were used on these files to try to crack their passwords. Second, interviews with 20 study coordinators were conducted to understand file-sharing practices in clinical trials for files containing personal health information. We were able to crack the passwords for 93% of the files (14/15). Among these, 13 files contained thousands of records with sensitive health information on trial participants. The passwords tended to be relatively weak, using common names of locations, animals, car brands, and obvious numeric sequences. Patient information is commonly shared by email in the context of query resolution. Files containing personal health information are shared by email and, by posting them on shared drives with common passwords, to facilitate collaboration. If files containing sensitive patient information must be transferred by email, mechanisms to encrypt them and to ensure that password strength is high are necessary. More sophisticated collaboration tools are required to allow file sharing without password sharing. We provide recommendations to implement these practices.

How Strong are Passwords Used to Protect Personal Health Information in Clinical Trials?

PubMed Central

Moreau, Katherine; Jonker, Elizabeth

2011-01-01

Background Findings and statements about how securely personal health information is managed in clinical research are mixed. Objective The objective of our study was to evaluate the security of practices used to transfer and share sensitive files in clinical trials. Methods Two studies were performed. First, 15 password-protected files that were transmitted by email during regulated Canadian clinical trials were obtained. Commercial password recovery tools were used on these files to try to crack their passwords. Second, interviews with 20 study coordinators were conducted to understand file-sharing practices in clinical trials for files containing personal health information. Results We were able to crack the passwords for 93% of the files (14/15). Among these, 13 files contained thousands of records with sensitive health information on trial participants. The passwords tended to be relatively weak, using common names of locations, animals, car brands, and obvious numeric sequences. Patient information is commonly shared by email in the context of query resolution. Files containing personal health information are shared by email and, by posting them on shared drives with common passwords, to facilitate collaboration. Conclusion If files containing sensitive patient information must be transferred by email, mechanisms to encrypt them and to ensure that password strength is high are necessary. More sophisticated collaboration tools are required to allow file sharing without password sharing. We provide recommendations to implement these practices. PMID:21317106

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...

Layout-aware text extraction from full-text PDF of scientific articles.

PubMed

Ramakrishnan, Cartic; Patnia, Abhishek; Hovy, Eduard; Burns, Gully Apc

2012-05-28

The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the 'Layout-Aware PDF Text Extraction' (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/.

Layout-aware text extraction from full-text PDF of scientific articles

PubMed Central

2012-01-01

Background The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the ‘Layout-Aware PDF Text Extraction’ (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Results Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. Conclusions LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/. PMID:22640904

Who Goes There? Measuring Library Web Site Usage.

ERIC Educational Resources Information Center

Bauer, Kathleen

2000-01-01

Discusses how libraries can gather data on the use of their Web sites. Highlights include Web server log files, including the common log file, referrer log file, and agent log file; log file limitations; privacy concerns; and choosing log analysis software, both free and commercial. (LRW)

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.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Perl One-Liners: Bridging the Gap Between Large Data Sets and Analysis Tools.

PubMed

Hokamp, Karsten

2015-01-01

Computational analyses of biological data are becoming increasingly powerful, and researchers intending on carrying out their own analyses can often choose from a wide array of tools and resources. However, their application might be obstructed by the wide variety of different data formats that are in use, from standard, commonly used formats to output files from high-throughput analysis platforms. The latter are often too large to be opened, viewed, or edited by standard programs, potentially leading to a bottleneck in the analysis. Perl one-liners provide a simple solution to quickly reformat, filter, and merge data sets in preparation for downstream analyses. This chapter presents example code that can be easily adjusted to meet individual requirements. An online version is available at http://bioinf.gen.tcd.ie/pol.

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.

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.

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).

Strategies for Sharing Seismic Data Among Multiple Computer Platforms

NASA Astrophysics Data System (ADS)

Baker, L. M.; Fletcher, J. B.

2001-12-01

Seismic waveform data is readily available from a variety of sources, but it often comes in a distinct, instrument-specific data format. For example, data may be from portable seismographs, such as those made by Refraction Technology or Kinemetrics, from permanent seismograph arrays, such as the USGS Parkfield Dense Array, from public data centers, such as the IRIS Data Center, or from personal communication with other researchers through e-mail or ftp. A computer must be selected to import the data - usually whichever is the most suitable for reading the originating format. However, the computer best suited for a specific analysis may not be the same. When copies of the data are then made for analysis, a proliferation of copies of the same data results, in possibly incompatible, computer-specific formats. In addition, if an error is detected and corrected in one copy, or some other change is made, all the other copies must be updated to preserve their validity. Keeping track of what data is available, where it is located, and which copy is authoritative requires an effort that is easy to neglect. We solve this problem by importing waveform data to a shared network file server that is accessible to all our computers on our campus LAN. We use a Network Appliance file server running Sun's Network File System (NFS) software. Using an NFS client software package on each analysis computer, waveform data can then be read by our MatLab or Fortran applications without first copying the data. Since there is a single copy of the waveform data in a single location, the NFS file system hierarchy provides an implicit complete waveform data catalog and the single copy is inherently authoritative. Another part of our solution is to convert the original data into a blocked-binary format (known historically as USGS DR100 or VFBB format) that is interpreted by MatLab or Fortran library routines available on each computer so that the idiosyncrasies of each machine are not visible to the user. Commercial software packages, such as MatLab, also have the ability to share data in their own formats across multiple computer platforms. Our Fortran applications can create plot files in Adobe PostScript, Illustrator, and Portable Document Format (PDF) formats. Vendor support for reading these files is readily available on multiple computer platforms. We will illustrate by example our strategies for sharing seismic data among our multiple computer platforms, and we will discuss our positive and negative experiences. We will include our solutions for handling the different byte ordering, floating-point formats, and text file ``end-of-line'' conventions on the various computer platforms we use (6 different operating systems on 5 processor architectures).

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.

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...

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 ...

47 CFR 61.14 - Method of filing publications.

Code of Federal Regulations, 2010 CFR

2010-10-01

....14 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) TARIFFS Rules for Electronic Filing § 61.14 Method of filing publications. (a) Publications filed electronically must be addressed to “Secretary, Federal Communications Commission, Washington, DC 20554.” The...

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).

RCHILD - an R-package for flexible use of the landscape evolution model CHILD

NASA Astrophysics Data System (ADS)

Dietze, Michael

2014-05-01

Landscape evolution models provide powerful approaches to numerically assess earth surface processes, to quantify rates of landscape change, infer sediment transfer rates, estimate sediment budgets, investigate the consequences of changes in external drivers on a geomorphic system, to provide spatio-temporal interpolations between known landscape states or to test conceptual hypotheses. CHILD (Channel-Hillslope Integrated Landscape Development Model) is one of the most-used models of landscape change in the context of at least tectonic and geomorphologic process interactions. Running CHILD from command line and working with the model output can be a rather awkward task (static model control via text input file, only numeric output in text files). The package RCHILD is a collection of functions for the free statistical software R that help using CHILD in a flexible, dynamic and user-friendly way. The comprised functions allow creating maps, real-time scenes, animations and further thematic plots from model output. The model input files can be modified dynamically and, hence, (feedback-related) changes in external factors can be implemented iteratively. Output files can be written to common formats that can be readily imported to standard GIS software. This contribution presents the basic functionality of the model CHILD as visualised and modified by the package. A rough overview of the available functions is given. Application examples help to illustrate the great potential of numeric modelling of geomorphologic processes.

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.

Development of Software to Model AXAF-I Image Quality

NASA Technical Reports Server (NTRS)

Geary, Joseph; Hawkins, Lamar; Ahmad, Anees; Gong, Qian

1997-01-01

This report describes work conducted on Delivery Order 181 between October 1996 through June 1997. During this period software was written to: compute axial PSD's from RDOS AXAF-I mirror surface maps; plot axial surface errors and compute PSD's from HDOS "Big 8" axial scans; plot PSD's from FITS format PSD files; plot band-limited RMS vs axial and azimuthal position for multiple PSD files; combine and organize PSD's from multiple mirror surface measurements formatted as input to GRAZTRACE; modify GRAZTRACE to read FITS formatted PSD files; evaluate AXAF-I test results; improve and expand the capabilities of the GT x-ray mirror analysis package. During this period work began on a more user-friendly manual for the GT program, and improvements were made to the on-line help manual.

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.

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

Modifications of the U.S. Geological Survey modular, finite-difference, ground-water flow model to read and write geographic information system files

USGS Publications Warehouse

Orzol, Leonard L.; McGrath, Timothy S.

1992-01-01

This report documents modifications to the U.S. Geological Survey modular, three-dimensional, finite-difference, ground-water flow model, commonly called MODFLOW, so that it can read and write files used by a geographic information system (GIS). The modified model program is called MODFLOWARC. Simulation programs such as MODFLOW generally require large amounts of input data and produce large amounts of output data. Viewing data graphically, generating head contours, and creating or editing model data arrays such as hydraulic conductivity are examples of tasks that currently are performed either by the use of independent software packages or by tedious manual editing, manipulating, and transferring data. Programs such as GIS programs are commonly used to facilitate preparation of the model input data and analyze model output data; however, auxiliary programs are frequently required to translate data between programs. Data translations are required when different programs use different data formats. Thus, the user might use GIS techniques to create model input data, run a translation program to convert input data into a format compatible with the ground-water flow model, run the model, run a translation program to convert the model output into the correct format for GIS, and use GIS to display and analyze this output. MODFLOWARC, avoids the two translation steps and transfers data directly to and from the ground-water-flow model. This report documents the design and use of MODFLOWARC and includes instructions for data input/output of the Basic, Block-centered flow, River, Recharge, Well, Drain, Evapotranspiration, General-head boundary, and Streamflow-routing packages. The modification to MODFLOW and the Streamflow-Routing package was minimized. Flow charts and computer-program code describe the modifications to the original computer codes for each of these packages. Appendix A contains a discussion on the operation of MODFLOWARC using a sample problem.

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).

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.

Context-dependent JPEG backward-compatible high-dynamic range image compression

NASA Astrophysics Data System (ADS)

Korshunov, Pavel; Ebrahimi, Touradj

2013-10-01

High-dynamic range (HDR) imaging is expected, together with ultrahigh definition and high-frame rate video, to become a technology that may change photo, TV, and film industries. Many cameras and displays capable of capturing and rendering both HDR images and video are already available in the market. The popularity and full-public adoption of HDR content is, however, hindered by the lack of standards in evaluation of quality, file formats, and compression, as well as large legacy base of low-dynamic range (LDR) displays that are unable to render HDR. To facilitate the wide spread of HDR usage, the backward compatibility of HDR with commonly used legacy technologies for storage, rendering, and compression of video and images are necessary. Although many tone-mapping algorithms are developed for generating viewable LDR content from HDR, there is no consensus of which algorithm to use and under which conditions. We, via a series of subjective evaluations, demonstrate the dependency of the perceptual quality of the tone-mapped LDR images on the context: environmental factors, display parameters, and image content itself. Based on the results of subjective tests, it proposes to extend JPEG file format, the most popular image format, in a backward compatible manner to deal with HDR images also. An architecture to achieve such backward compatibility with JPEG is proposed. A simple implementation of lossy compression demonstrates the efficiency of the proposed architecture compared with the state-of-the-art HDR image compression.

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.

The digital curriculum vitae.

PubMed

Galdino, Greg M; Gotway, Michael

2005-02-01

The curriculum vitae (CV) has been the traditional method for radiologists to illustrate their accomplishments in the field of medicine. Despite its presence in medicine as a standard, widely accepted means to describe one's professional career and its use for decades as an accomplice to most applications and interviews, there is relatively little written in the medical literature regarding the CV. Misrepresentation on medical students', residents', and fellows' applications has been reported. Using digital technology, CVs have the potential to be much more than printed words on paper and offers a solution to misrepresentation. Digital CVs may incorporate full-length articles, graphics, presentations, clinical images, and video. Common formats for digital CVs include CD-ROMs or DVD-ROMs containing articles (in Adobe Portable Document Format) and presentations (in Microsoft PowerPoint format) accompanying printed CVs, word processing documents with hyperlinks to articles and presentations either locally (on CD-ROMs or DVD-ROMs) or remotely (via the Internet), or hypertext markup language documents. Digital CVs afford the ability to provide more information that is readily accessible to those receiving and reviewing them. Articles, presentations, videos, images, and Internet links can be illustrated using standard file formats commonly available to all radiologists. They can be easily updated and distributed on an inexpensive media, such as a CD-ROM or DVD-ROM. With the availability of electronic articles, presentations, and information via the Internet, traditional paper CVs may soon be superseded by their electronic successors.

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...

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.

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

PubMed Central

Wolfinger, Michael T.; Fallmann, Jörg; Eggenhofer, Florian; Amman, Fabian

2015-01-01

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools. PMID:26236465

Toolkit for testing scientific CCD cameras

NASA Astrophysics Data System (ADS)

Uzycki, Janusz; Mankiewicz, Lech; Molak, Marcin; Wrochna, Grzegorz

2006-03-01

The CCD Toolkit (1) is a software tool for testing CCD cameras which allows to measure important characteristics of a camera like readout noise, total gain, dark current, 'hot' pixels, useful area, etc. The application makes a statistical analysis of images saved in files with FITS format, commonly used in astronomy. A graphical interface is based on the ROOT package, which offers high functionality and flexibility. The program was developed in a way to ensure future compatibility with different operating systems: Windows and Linux. The CCD Toolkit was created for the "Pie of the Sky" project collaboration (2).

Visualizing NetCDF Files by Using the EverVIEW Data Viewer

USGS Publications Warehouse

Conzelmann, Craig; Romañach, Stephanie S.

2010-01-01

Over the past few years, modelers in South Florida have started using Network Common Data Form (NetCDF) as the standard data container format for storing hydrologic and ecologic modeling inputs and outputs. With its origins in the meteorological discipline, NetCDF was created by the Unidata Program Center at the University Corporation for Atmospheric Research, in conjunction with the National Aeronautics and Space Administration and other organizations. NetCDF is a portable, scalable, self-describing, binary file format optimized for storing array-based scientific data. Despite attributes which make NetCDF desirable to the modeling community, many natural resource managers have few desktop software packages which can consume NetCDF and unlock the valuable data contained within. The U.S. Geological Survey and the Joint Ecosystem Modeling group, an ecological modeling community of practice, are working to address this need with the EverVIEW Data Viewer. Available for several operating systems, this desktop software currently supports graphical displays of NetCDF data as spatial overlays on a three-dimensional globe and views of grid-cell values in tabular form. An included Open Geospatial Consortium compliant, Web-mapping service client and charting interface allows the user to view Web-available spatial data as additional map overlays and provides simple charting visualizations of NetCDF grid values.

Voxel2MCNP: a framework for modeling, simulation and evaluation of radiation transport scenarios for Monte Carlo codes.

PubMed

Pölz, Stefan; Laubersheimer, Sven; Eberhardt, Jakob S; Harrendorf, Marco A; Keck, Thomas; Benzler, Andreas; Breustedt, Bastian

2013-08-21

The basic idea of Voxel2MCNP is to provide a framework supporting users in modeling radiation transport scenarios using voxel phantoms and other geometric models, generating corresponding input for the Monte Carlo code MCNPX, and evaluating simulation output. Applications at Karlsruhe Institute of Technology are primarily whole and partial body counter calibration and calculation of dose conversion coefficients. A new generic data model describing data related to radiation transport, including phantom and detector geometries and their properties, sources, tallies and materials, has been developed. It is modular and generally independent of the targeted Monte Carlo code. The data model has been implemented as an XML-based file format to facilitate data exchange, and integrated with Voxel2MCNP to provide a common interface for modeling, visualization, and evaluation of data. Also, extensions to allow compatibility with several file formats, such as ENSDF for nuclear structure properties and radioactive decay data, SimpleGeo for solid geometry modeling, ImageJ for voxel lattices, and MCNPX's MCTAL for simulation results have been added. The framework is presented and discussed in this paper and example workflows for body counter calibration and calculation of dose conversion coefficients is given to illustrate its application.

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...

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

Mynodbcsv: lightweight zero-config database solution for handling very large CSV files.

PubMed

Adaszewski, Stanisław

2014-01-01

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: "no copy" approach--data stay mostly in the CSV files; "zero configuration"--no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results.

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.

Mynodbcsv: Lightweight Zero-Config Database Solution for Handling Very Large CSV Files

PubMed Central

Adaszewski, Stanisław

2014-01-01

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: “no copy” approach – data stay mostly in the CSV files; “zero configuration” – no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results. PMID:25068261

QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories

PubMed Central

Chiva, Cristina; Olivella, Roger; Borràs, Eva; Espadas, Guadalupe; Pastor, Olga; Solé, Amanda

2018-01-01

The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts to set standard file formats, data processing workflows and key evaluation parameters for quality control, automated quality control systems are not yet widespread among proteomics laboratories, which limits the acquisition of high-quality results, inter-laboratory comparisons and the assessment of variability of instrumental platforms. Here we present QCloud, a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation. QCloud supports the most common targeted and untargeted proteomics workflows, it accepts data formats from different vendors and it enables the annotation of acquired data and reporting incidences. A complete version of the QCloud system has successfully been developed and it is now open to the proteomics community (http://qcloud.crg.eu). QCloud system is an open source project, publicly available under a Creative Commons License Attribution-ShareAlike 4.0. PMID:29324744

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M.; Le Novére, Nicolas; Myers, Chris J.; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Waltemath, Dagmar; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528569

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Hoops, Stefan; Keating, Sarah M.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528564

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

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.

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.

Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant.

PubMed

Kovalchik, Kevin A; Moggridge, Sophie; Chen, David D Y; Morin, Gregg B; Hughes, Christopher S

2018-06-01

Effective analysis of protein samples by mass spectrometry (MS) requires careful selection and optimization of a range of experimental parameters. As the output from the primary detection device, the "raw" MS data file can be used to gauge the success of a given sample analysis. However, the closed-source nature of the standard raw MS file can complicate effective parsing of the data contained within. To ease and increase the range of analyses possible, the RawQuant tool was developed to enable parsing of raw MS files derived from Thermo Orbitrap instruments to yield meta and scan data in an openly readable text format. RawQuant can be commanded to export user-friendly files containing MS 1 , MS 2 , and MS 3 metadata as well as matrices of quantification values based on isobaric tagging approaches. In this study, the utility of RawQuant is demonstrated in several scenarios: (1) reanalysis of shotgun proteomics data for the identification of the human proteome, (2) reanalysis of experiments utilizing isobaric tagging for whole-proteome quantification, and (3) analysis of a novel bacterial proteome and synthetic peptide mixture for assessing quantification accuracy when using isobaric tags. Together, these analyses successfully demonstrate RawQuant for the efficient parsing and quantification of data from raw Thermo Orbitrap MS files acquired in a range of common proteomics experiments. In addition, the individual analyses using RawQuant highlights parametric considerations in the different experimental sets and suggests targetable areas to improve depth of coverage in identification-focused studies and quantification accuracy when using isobaric tags.

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).

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…

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.

ZOOM Lite: next-generation sequencing data mapping and visualization software

PubMed Central

Zhang, Zefeng; Lin, Hao; Ma, Bin

2010-01-01

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/. PMID:20530531

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.

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.

CUTSETS - MINIMAL CUT SET CALCULATION FOR DIGRAPH AND FAULT TREE RELIABILITY MODELS

NASA Technical Reports Server (NTRS)

Iverson, D. L.

1994-01-01

Fault tree and digraph models are frequently used for system failure analysis. Both type of models represent a failure space view of the system using AND and OR nodes in a directed graph structure. Fault trees must have a tree structure and do not allow cycles or loops in the graph. Digraphs allow any pattern of interconnection between loops in the graphs. A common operation performed on digraph and fault tree models is the calculation of minimal cut sets. A cut set is a set of basic failures that could cause a given target failure event to occur. A minimal cut set for a target event node in a fault tree or digraph is any cut set for the node with the property that if any one of the failures in the set is removed, the occurrence of the other failures in the set will not cause the target failure event. CUTSETS will identify all the minimal cut sets for a given node. The CUTSETS package contains programs that solve for minimal cut sets of fault trees and digraphs using object-oriented programming techniques. These cut set codes can be used to solve graph models for reliability analysis and identify potential single point failures in a modeled system. The fault tree minimal cut set code reads in a fault tree model input file with each node listed in a text format. In the input file the user specifies a top node of the fault tree and a maximum cut set size to be calculated. CUTSETS will find minimal sets of basic events which would cause the failure at the output of a given fault tree gate. The program can find all the minimal cut sets of a node, or minimal cut sets up to a specified size. The algorithm performs a recursive top down parse of the fault tree, starting at the specified top node, and combines the cut sets of each child node into sets of basic event failures that would cause the failure event at the output of that gate. Minimal cut set solutions can be found for all nodes in the fault tree or just for the top node. The digraph cut set code uses the same techniques as the fault tree cut set code, except it includes all upstream digraph nodes in the cut sets for a given node and checks for cycles in the digraph during the solution process. CUTSETS solves for specified nodes and will not automatically solve for all upstream digraph nodes. The cut sets will be output as a text file. CUTSETS includes a utility program that will convert the popular COD format digraph model description files into text input files suitable for use with the CUTSETS programs. FEAT (MSC-21873) and FIRM (MSC-21860) available from COSMIC are examples of programs that produce COD format digraph model description files that may be converted for use with the CUTSETS programs. CUTSETS is written in C-language to be machine independent. It has been successfully implemented on a Sun running SunOS, a DECstation running ULTRIX, a Macintosh running System 7, and a DEC VAX running VMS. The RAM requirement varies with the size of the models. CUTSETS is available in UNIX tar format on a .25 inch streaming magnetic tape cartridge (standard distribution) or on a 3.5 inch diskette. It is also available on a 3.5 inch Macintosh format diskette or on a 9-track 1600 BPI magnetic tape in DEC VAX FILES-11 format. Sample input and sample output are provided on the distribution medium. An electronic copy of the documentation in Macintosh Microsoft Word format is included on the distribution medium. Sun and SunOS are trademarks of Sun Microsystems, Inc. DEC, DeCstation, ULTRIX, VAX, and VMS are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories. Macintosh is a registered trademark of Apple Computer, Inc.

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.

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

LipidMiner: A Software for Automated Identification and Quantification of Lipids from Multiple Liquid Chromatography-Mass Spectrometry Data Files

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

Meng, Da; Zhang, Qibin; Gao, Xiaoli

2014-04-30

We have developed a tool for automated, high-throughput analysis of LC-MS/MS data files, which greatly simplifies LC-MS based lipidomics analysis. Our results showed that LipidMiner is accurate and comprehensive in identification and quantification of lipid molecular species. In addition, the workflow implemented in LipidMiner is not limited to identification and quantification of lipids. If a suitable metabolite library is implemented in the library matching module, LipidMiner could be reconfigured as a tool for general metabolomics data analysis. It is of note that LipidMiner currently is limited to singly charged ions, although it is adequate for the purpose of lipidomics sincemore » lipids are rarely multiply charged,[14] even for the polyphosphoinositides. LipidMiner also only processes file formats generated from mass spectrometers from Thermo, i.e. the .RAW format. In the future, we are planning to accommodate file formats generated by mass spectrometers from other predominant instrument vendors to make this tool more universal.« less

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.

40 CFR 22.5 - Filing, service, and form of all filed documents; business confidentiality claims.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 1 2013-07-01 2013-07-01 false Filing, service, and form of all filed... PENALTIES AND THE REVOCATION/TERMINATION OR SUSPENSION OF PERMITS General § 22.5 Filing, service, and form... association which is subject to suit under a common name, complainant shall serve an officer, partner, a...

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

PubMed

Sanderson, Lacey-Anne; Ficklin, Stephen P; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A; Bett, Kirstin E; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

PubMed Central

Sanderson, Lacey-Anne; Ficklin, Stephen P.; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A.; Bett, Kirstin E.; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including ‘Feature Map’, ‘Genetic’, ‘Publication’, ‘Project’, ‘Contact’ and the ‘Natural Diversity’ modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. Database URL: http://tripal.info/ PMID:24163125

The Northern Circumpolar Soil Carbon Database: spatially distributed datasets of soil coverage and soil carbon storage in the northern permafrost regions

NASA Astrophysics Data System (ADS)

Hugelius, G.; Tarnocai, C.; Broll, G.; Canadell, J. G.; Kuhry, P.; Swanson, D. K.

2012-08-01

High latitude terrestrial ecosystems are key components in the global carbon (C) cycle. Estimates of global soil organic carbon (SOC), however, do not include updated estimates of SOC storage in permafrost-affected soils or representation of the unique pedogenic processes that affect these soils. The Northern Circumpolar Soil Carbon Database (NCSCD) was developed to quantify the SOC stocks in the circumpolar permafrost region (18.7 × 106 km2). The NCSCD is a polygon-based digital database compiled from harmonized regional soil classification maps in which data on soil order coverage has been linked to pedon data (n = 1647) from the northern permafrost regions to calculate SOC content and mass. In addition, new gridded datasets at different spatial resolutions have been generated to facilitate research applications using the NCSCD (standard raster formats for use in Geographic Information Systems and Network Common Data Form files common for applications in numerical models). This paper describes the compilation of the NCSCD spatial framework, the soil sampling and soil analyses procedures used to derive SOC content in pedons from North America and Eurasia and the formatting of the digital files that are available online. The potential applications and limitations of the NCSCD in spatial analyses are also discussed. The database has the doi:10.5879/ecds/00000001. An open access data-portal with all the described GIS-datasets is available online at: http://dev1.geo.su.se/bbcc/dev/ncscd/.

The Northern Circumpolar Soil Carbon Database: spatially distributed datasets of soil coverage and soil carbon storage in the northern permafrost regions

NASA Astrophysics Data System (ADS)

Hugelius, G.; Tarnocai, C.; Broll, G.; Canadell, J. G.; Kuhry, P.; Swanson, D. K.

2013-01-01

High-latitude terrestrial ecosystems are key components in the global carbon (C) cycle. Estimates of global soil organic carbon (SOC), however, do not include updated estimates of SOC storage in permafrost-affected soils or representation of the unique pedogenic processes that affect these soils. The Northern Circumpolar Soil Carbon Database (NCSCD) was developed to quantify the SOC stocks in the circumpolar permafrost region (18.7 × 106 km2). The NCSCD is a polygon-based digital database compiled from harmonized regional soil classification maps in which data on soil order coverage have been linked to pedon data (n = 1778) from the northern permafrost regions to calculate SOC content and mass. In addition, new gridded datasets at different spatial resolutions have been generated to facilitate research applications using the NCSCD (standard raster formats for use in geographic information systems and Network Common Data Form files common for applications in numerical models). This paper describes the compilation of the NCSCD spatial framework, the soil sampling and soil analytical procedures used to derive SOC content in pedons from North America and Eurasia and the formatting of the digital files that are available online. The potential applications and limitations of the NCSCD in spatial analyses are also discussed. The database has the doi:10.5879/ecds/00000001. An open access data portal with all the described GIS-datasets is available online at: http://www.bbcc.su.se/data/ncscd/.

47 CFR 61.13 - Scope.

Code of Federal Regulations, 2010 CFR

2010-10-01

... FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) TARIFFS Rules for Electronic Filing § 61.13 Scope. (a) This applies to all tariff publications of carriers required to file... technical requirements of the Electronic Tariff Filing System. ...

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.

Kubios HRV--heart rate variability analysis software.

PubMed

Tarvainen, Mika P; Niskanen, Juha-Pekka; Lipponen, Jukka A; Ranta-Aho, Perttu O; Karjalainen, Pasi A

2014-01-01

Kubios HRV is an advanced and easy to use software for heart rate variability (HRV) analysis. The software supports several input data formats for electrocardiogram (ECG) data and beat-to-beat RR interval data. It includes an adaptive QRS detection algorithm and tools for artifact correction, trend removal and analysis sample selection. The software computes all the commonly used time-domain and frequency-domain HRV parameters and several nonlinear parameters. There are several adjustable analysis settings through which the analysis methods can be optimized for different data. The ECG derived respiratory frequency is also computed, which is important for reliable interpretation of the analysis results. The analysis results can be saved as an ASCII text file (easy to import into MS Excel or SPSS), Matlab MAT-file, or as a PDF report. The software is easy to use through its compact graphical user interface. The software is available free of charge for Windows and Linux operating systems at http://kubios.uef.fi. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

BEASTling: A software tool for linguistic phylogenetics using BEAST 2

PubMed Central

Forkel, Robert; Kaiping, Gereon A.; Atkinson, Quentin D.

2017-01-01

We present a new open source software tool called BEASTling, designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform. BEASTling transforms comparatively short and human-readable configuration files into the XML files used by BEAST to specify analyses. By taking advantage of Creative Commons-licensed data from the Glottolog language catalog, BEASTling allows the user to conveniently filter datasets using names for recognised language families, to impose monophyly constraints so that inferred language trees are backward compatible with Glottolog classifications, or to assign geographic location data to languages for phylogeographic analyses. Support for the emerging cross-linguistic linked data format (CLDF) permits easy incorporation of data published in cross-linguistic linked databases into analyses. BEASTling is intended to make the power of Bayesian analysis more accessible to historical linguists without strong programming backgrounds, in the hopes of encouraging communication and collaboration between those developing computational models of language evolution (who are typically not linguists) and relevant domain experts. PMID:28796784

BEASTling: A software tool for linguistic phylogenetics using BEAST 2.

PubMed

Maurits, Luke; Forkel, Robert; Kaiping, Gereon A; Atkinson, Quentin D

2017-01-01

We present a new open source software tool called BEASTling, designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform. BEASTling transforms comparatively short and human-readable configuration files into the XML files used by BEAST to specify analyses. By taking advantage of Creative Commons-licensed data from the Glottolog language catalog, BEASTling allows the user to conveniently filter datasets using names for recognised language families, to impose monophyly constraints so that inferred language trees are backward compatible with Glottolog classifications, or to assign geographic location data to languages for phylogeographic analyses. Support for the emerging cross-linguistic linked data format (CLDF) permits easy incorporation of data published in cross-linguistic linked databases into analyses. BEASTling is intended to make the power of Bayesian analysis more accessible to historical linguists without strong programming backgrounds, in the hopes of encouraging communication and collaboration between those developing computational models of language evolution (who are typically not linguists) and relevant domain experts.

BioSAVE: display of scored annotation within a sequence context.

PubMed

Pollock, Richard F; Adryan, Boris

2008-03-20

Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage.

BioSAVE: Display of scored annotation within a sequence context

PubMed Central

Pollock, Richard F; Adryan, Boris

2008-01-01

Background Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. Results We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Conclusion Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage. PMID:18366701

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.

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.

FPT- FORTRAN PROGRAMMING TOOLS FOR THE DEC VAX

NASA Technical Reports Server (NTRS)

Ragosta, A. E.

1994-01-01

The FORTRAN Programming Tools (FPT) are a series of tools used to support the development and maintenance of FORTRAN 77 source codes. Included are a debugging aid, a CPU time monitoring program, source code maintenance aids, print utilities, and a library of useful, well-documented programs. These tools assist in reducing development time and encouraging high quality programming. Although intended primarily for FORTRAN programmers, some of the tools can be used on data files and other programming languages. BUGOUT is a series of FPT programs that have proven very useful in debugging a particular kind of error and in optimizing CPU-intensive codes. The particular type of error is the illegal addressing of data or code as a result of subtle FORTRAN errors that are not caught by the compiler or at run time. A TRACE option also allows the programmer to verify the execution path of a program. The TIME option assists the programmer in identifying the CPU-intensive routines in a program to aid in optimization studies. Program coding, maintenance, and print aids available in FPT include: routines for building standard format subprogram stubs; cleaning up common blocks and NAMELISTs; removing all characters after column 72; displaying two files side by side on a VT-100 terminal; creating a neat listing of a FORTRAN source code including a Table of Contents, an Index, and Page Headings; converting files between VMS internal format and standard carriage control format; changing text strings in a file without using EDT; and replacing tab characters with spaces. The library of useful, documented programs includes the following: time and date routines; a string categorization routine; routines for converting between decimal, hex, and octal; routines to delay process execution for a specified time; a Gaussian elimination routine for solving a set of simultaneous linear equations; a curve fitting routine for least squares fit to polynomial, exponential, and sinusoidal forms (with a screen-oriented editor); a cubic spline fit routine; a screen-oriented array editor; routines to support parsing; and various terminal support routines. These FORTRAN programming tools are written in FORTRAN 77 and ASSEMBLER for interactive and batch execution. FPT is intended for implementation on DEC VAX series computers operating under VMS. This collection of tools was developed in 1985.

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 ...

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).

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.

The successful implementation of a licensed data management interface between a Sunquest(®) laboratory information system and an AB SCIEX™ mass spectrometer.

PubMed

French, Deborah; Terrazas, Enrique

2013-01-01

Interfacing complex laboratory equipment to laboratory information systems (LIS) has become a more commonly encountered problem in clinical laboratories, especially for instruments that do not have an interface provided by the vendor. Liquid chromatography-tandem mass spectrometry is a great example of such complex equipment, and has become a frequent addition to clinical laboratories. As the testing volume on such instruments can be significant, manual data entry will also be considerable and the potential for concomitant transcription errors arises. Due to this potential issue, our aim was to interface an AB SCIEX™ mass spectrometer to our Sunquest(®) LIS. WE LICENSED SOFTWARE FOR THE DATA MANAGEMENT INTERFACE FROM THE UNIVERSITY OF PITTSBURGH, BUT EXTENDED THIS WORK AS FOLLOWS: The interface was designed so that it would accept a text file exported from the AB SCIEX™ × 5500 QTrap(®) mass spectrometer, pre-process the file (using newly written code) into the correct format and upload it into Sunquest(®) via file transfer protocol. The licensed software handled the majority of the interface tasks with the exception of converting the output from the Analyst(®) software to the required Sunquest(®) import format. This required writing of a "pre-processor" by one of the authors which was easily integrated with the supplied software. We successfully implemented the data management interface licensed from the University of Pittsburgh. Given the coding that was required to write the pre-processor, and alterations to the source code that were performed when debugging the software, we would suggest that before a laboratory decides to implement such an interface, it would be necessary to have a competent computer programmer available.

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...

76 FR 2897 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-18

... Assignment, Contenancy and Common Facilities Agreement with Succession to be effective 10/14/2010. Filed Date... Energy LLC submits tariff filing per 35: Amendment to Market-Based Rate Tariff 01062011 to be effective 1... Succession to be effective 2/9/2011. Filed Date: 01/06/2011. Accession Number: 20110106-5096. Comment Date: 5...

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.

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

International Conference on Harmonisation; guidance on the M4 Common Technical Document--Quality: Questions and Answers/Location Issues; availability. Notice.

PubMed

2004-06-09

The Food and Drug Administration (FDA) is announcing the availability of a guidance entitled "M4: The CTD--Quality: Questions and Answers/Location Issues." The guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). This guidance provides further clarification for preparing the quality components of an application file in the common technical document (CTD) format. The guidance addresses the relationship between linked sections for certain parameters (such as polymorphism and particle size), and it addresses location issues (by indicating the section in which to place requested information). The guidance is intended to ease the preparation of paper and electronic submissions, facilitate regulatory reviews, and simplify the exchange of regulatory information among regulatory authorities.

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).

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.

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.

76 FR 80866 - Non-Vessel-Operating Common Carriers Negotiated Rate Arrangements; Tariff Filing Exemption

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-27

... FEDERAL MARITIME COMMISSION 46 CFR Part 532 [Docket No. 11-22] Non-Vessel-Operating Common Carriers Negotiated Rate Arrangements; Tariff Filing Exemption AGENCY: Federal Maritime Commission. ACTION: Notice of Inquiry. SUMMARY: The Federal Maritime Commission is issuing this Notice of Inquiry seeking...

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.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

PubMed

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

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