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Phase III: Implementation and Operation of the Repository

Description: The metadata catalog was brought online for public access May 14, 1998. Since then dozens of users have registered and began to access the system. The system was demonstrated at the AAPG annual meeting in Salt Lake City and the EAGE (European Association of Geoscientists and Engineers) annual meeting in Leipzig, Germany. Hart Publications and PTTC �NetworkNews� have published articles about the metadata catalog, and articles for the AAPG Explorer and GSA Today are being developed. A back-up system at AGI headquarters was established. In support of the metadata catalog system, a leased-line Internet connection and two servers were installed. Porting of the GeoTrek server software to the new systems has begun. The back-up system will be operational during the 3 rd quarter of 1998 and will serve the NGDRS needs during periods when access to the site in Houston is down. Additionally, experimentation with new data types and deployment schemes will be tested on the system at AGI. The NGDRS has picked-up additional endorsements from the American Association of State Geologists, the MMS Outer Continental Shelf Policy Committee, and a new endorsement is being formulated by the AAPG Core Preservation Committee for consideration by the AAPG Executive Committee. The Texas Bureau of Economic Geology (BEG) is currently geocoding the well locations for the metadata catalog. Also, they have solicited proposals for the development of a core inventory control system that will work hand-in-hand with GeoTrek. A contract for that system will probably be given during the 3 rd quarter of 1998. The Texas Railroad Commission proposes to test the application of GeoTrek for accessing data in a joint project with the BEG. Several data transfer projects are underway. Vastar has committed to the transfer of 2D Appalachian seismic lines to the NDGRS clearinghouse. Receiving repositories have been identified and ...
Date: July 1, 1998
Partner: UNT Libraries Government Documents Department

Phase III: Implementation and Operation of the Repository

Description: All of the hardware is installed and all available databases are loaded into the metadata repository. The final stages of beta testing of GeoTrek and necessary revisions are underway, with a targeted public release of the NGDRS system in April or May 1998. The Eastern Gulf Region PTTC, Oklahoma Geological Survey, and A2D databases have been converted and loaded into the metadata repository. These are in addition to the four previously installed databases, including the BEG, MMS, PGS, and Fairfield. Data quality improvements, particularly with the MMS and BEG data is continuing, including making the data more intuitive for the typical user. The beta-testing process has resulted in a number of action items that have been reviewed and addressed. Most of these issues have been resolved, and the remaining issues will be resolved early in the second quarter of 1998, leading to the public launch of the NGDRS metadata repository. Installation of GeoTrek at the BEG, in an effort to bring their core holdings into the NDGRS, was completed in December. A review was held concerning the experiences of the BEG with GeoTrek during January. The feedback was largely positive, with only a couple technical details to address. A number of companies have also expressed interest and/or are evaluating PetroTrek, the commercial version of GeoTrek. Thus far, most of those companies, including PGS and Fairfield, which have licensed PetroTrek have simultaneously joined the NGDRS as well. Several data transfer efforts are underway. Vastar has committed to the transfer of 2D Appalachian seismic lines to the NDGRS clearinghouse. Receiving repositories have been identified and the final preparations are being made for transfer to these public repositories. Additionally, discussions continue with the Stapleton Development Corporation concerning the transfer of facilities in Denver for use as a central core repository.
Date: April 1, 1998
Partner: UNT Libraries Government Documents Department

Phase III: Implementation and Operation of the repository

Description: In October all three Sun servers (3000, Ultra/II) were loaded, and we were able to demonstrate the complete system � databases, web front-page, and GeoTrek � to a large audience. All systems required for the web-based metadata catalog are in place and operational. Version 54 of the PetroTrek/GeoTrek software was loaded in December and is being tested. It is expected this version will be placed in the production environment for beta testing in January. Installation of the Bureau of Economic Geology (BEG) databases on the IS Houston server was completed and GeoTrek was loaded on BEG�s server in Austin. Installation of the entire MMS well data set (35,000 records) was completed and it will be moved to the production environment for beta testing in January. The Eastern Gulf Region PTTC interior salt basin data set was prepared and it will be loaded in January. The Gulf of Mexico PGS seismic data set was prepared and loaded in December. The web-site front pages for the NGDRS GeoTrek Metadata Catalog are 70 percent completed and write-ups for the tutorials are scheduled to be completed in January. Ten users identified to be beta testers are actively testing the system.
Date: January 1, 1998
Partner: UNT Libraries Government Documents Department

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

Description: The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.
Date: July 23, 2009
Creator: Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V. & Dubchak, Inna
Partner: UNT Libraries Government Documents Department

Protein Data Bank Project at Rutgers University

Description: The central activities of the Protein Data Base continue to be the collection, archiving and distribution of high quality structural data to the scientific community on a timely basis. The systems that have been developed for doing this has become increasingly reliable and stable. We have completed the inventory of magnetic and paper media that was received from Brookhaven National Laboratory.
Date: July 18, 2002
Creator: Berman, Helen
Partner: UNT Libraries Government Documents Department

Midland Core Repository

Description: The facility continues to be organized and data continue to be entered into the same database that contains the Austin facility�s information. This is expected to continue throughout FY98. The roof has new been repaired.
Date: April 1, 1998
Creator: Tyler, Noel
Partner: UNT Libraries Government Documents Department

Calibration of the MACHO photometry database

Description: The MACHO Project is a microlensing survey that monitors the brightnesses of -60 million stars in the Large Magellanic Cloud (LMC), Small Magellanic Cloud, and Galactic bulge. The database presently contains more photometric measurements than previously recorded in the history of astronomy. We describe the calibration of the MACHO two-color photometry and transformation to the standard Kron-Cousins V and R system. This allows for proper comparison with all other observations on the Kron-Cousins standard system. The highest precision calibrations are for -9 million stars in the LMC bar. For these stars, independent photometric measurements in field-overlap regions indicate standard deviations {sigma}{sub V} = {sigma}{sub R} = 0.020 mag. Calibrated MACHO photometry data are compared with published photometric sequences and with new Hubble Space Telescope observations. We additionally describe the first application of these calibrated data: the construction of the �efficiency� color-magnitude diagram which will be used to calculate our experimental sensitivity for detecting microlensing in the LMC.
Date: October 23, 1998
Creator: Alcock, A.
Partner: UNT Libraries Government Documents Department


Description: This project generates and provides coal samples and accompanying analytical data for research by DOE contractors and others. The five-year contract has been completed and a six-month no-cost extension is under way; this will continue the limited distribution of samples and data to DOE, its contractors and grantees. All activities specified under the five-year contract have been completed. Eleven DECS samples were collected, processed to a variety of particle sizes, heat-sealed in foil laminate bags under argon, and placed in refrigerated storage. All were analyzed for basic chemical composition, inorganic major and trace element composition including hazardous air pollutant elements, petrographic composition and characteristics, thermoplastic behavior (if applicable), and other properties relevant to commercial utilization. Most were also analyzed by NMR, py/gc/ms, and a standardized liquefaction test; trends and relationships observed were evaluated and summarized. Twenty-two DECS samples collected under the previous contract received further processing, and most of these were subjected to organic geochemical and standardized liquefaction tests as well. Selected DECS samples were monitored annually to evaluate the effectiveness of foil laminate bags for long-term sample storage. Twenty-three PSOC samples collected under previous contracts and purged with argon before storage were also maintained and distributed, for a total of 56 samples covered by the contract. During the five years, 524 samples in 1501 containers, 2075 data printouts, and individual data items from 30327 samples were distributed. In the subject quarter, 45 samples, 101 data printouts, and individual data items from 1237 samples were distributed. Splits of the last two samples from the previous contract received processing to minus 0.25 mm; all DECS samples are now available for immediate distribution at minus 6 mm (-1/4 inch), minus 0.85 mm (- 20 mesh U.S.), and minus 0.25 mm (minus 60 mesh U.S.). The final annual monitoring of foil laminate bag ...
Date: October 1, 1998
Partner: UNT Libraries Government Documents Department


Description: This project provides coal samples and accompanying analytical data for research by DOE contractors and others. All 56 samples have been purged with argon before storage, and the 33 samples in the DECS series are heat-sealed in foil laminate bags and stored under refrigeration. Eleven DECS samples have been collected under the current contract. The program of organic geochemical analyses for the contract was completed during the quarter, and its results (pyrolysis-GC/MS, and NMR spectroscopy by CPMAS and DDMAS) on 21 samples as well as standardized liquefaction results on 28 samples are summarized in this report. Samples and data continue to be distributed from the DOE Coal Sample Bank and Database to other DOE contractors.
Date: April 30, 1997
Creator: Davis, Alan & Glick, David C.
Partner: UNT Libraries Government Documents Department

The Sloan Digital Sky Survey data acquisition system, and early results

Description: The Sloan Digital Sky Survey will systematically map one- quarter of the sky, producing detailed images in five color bands and determining the positions and absolute bright- nesses of more than 100 million celestial objects. It will also measure the redshifts of a million selected galaxies and of 100,000 quasars, yielding a three-dimensional map of the universe through a volume one hundred times larger than that explored to date. The SDSS collaboration is currently in the process of commissioning the 2.5-meter survey tele- scope. We describe the data acquisition system used to record the survey data. This system consists of twelve sin- gle board computers and their associated interfaces to the camera and spectrograph CCD electronics, to tape drives, and to online video displays, distributed among several VME crates. A central UNIX computer connected to the VME crates via a vertical bus adapter coordinates the sys- tem and provides the interface to telescope operations. We briefly discuss results from the observing runs to date and plans for the archiving and distribution of data.
Date: June 29, 1999
Creator: J. Annis, J. Bakken, D. Holmgren, D. Petravick, R. Rechenmacher
Partner: UNT Libraries Government Documents Department

Atmospheric Radiation Measurement Climate Research Facility Operations Quarterly Report January 1–March 31, 2012

Description: Individual raw datastreams from instrumentation at the Atmospheric Radiation Measurement (ARM) Climate Research Facility fixed and mobile sites are collected and sent to the Data Management Facility (DMF) at Pacific Northwest National Laboratory (PNNL) for processing in near real-time. Raw and processed data are then sent approximately daily to the ARM Data Archive, where they are made available to the research community. For each instrument, we calculate the ratio of the actual number of processed data records received daily at the Archive to the expected number of data records. The results are tabulated by (1) individual datastream, site, and month for the current year and (2) site and fiscal year (FY) dating back to 1998.
Date: April 13, 2012
Creator: Voyles, J. W.
Partner: UNT Libraries Government Documents Department

INSPIRE and SPIRES Log File Analysis

Description: SPIRES, an aging high-energy physics publication data base, is in the process of being replaced by INSPIRE. In order to ease the transition from SPIRES to INSPIRE it is important to understand user behavior and the drivers for adoption. The goal of this project was to address some questions in regards to the presumed two-thirds of the users still using SPIRES. These questions are answered through analysis of the log files from both websites. A series of scripts were developed to collect and interpret the data contained in the log files. The common search patterns and usage comparisons are made between INSPIRE and SPIRES, and a method for detecting user frustration is presented. The analysis reveals a more even split than originally thought as well as the expected trend of user transition to INSPIRE.
Date: August 31, 2012
Creator: Adams, Cole & /SLAC, /Wheaton Coll.
Partner: UNT Libraries Government Documents Department

NNDC Data Services

Description: The National Nuclear Data Center has provided remote access to some of its resources since 1986. The major databases and other resources available currently through NNDC Web site are summarized. The National Nuclear Data Center (NNDC) has provided remote access to the nuclear physics databases it maintains and to other resources since 1986. With considerable innovation access is now mostly through the Web. The NNDC Web pages have been modernized to provide a consistent state-of-the-art style. The improved database services and other resources available from the NNOC site at www.nndc.bnl.govwill be described.
Date: April 30, 2010
Creator: Tuli, J.K. & Sonzogni,A.
Partner: UNT Libraries Government Documents Department

Multi-Petabyte Image Data Management Systems

Description: This research effort is directed to determine the methods and computational infrastructure needed to save, browse, and analyze multiple petabyte databases. The data set to be generated by the Large Synoptic Survey Telescope is used as a template for this research.
Date: January 29, 2007
Creator: Dossa, D D
Partner: UNT Libraries Government Documents Department

Department of Energy Project ER25739 Final Report “QoS-Enabled, High-performance Storage Systems for Data-Intensive Scientific Computing”

Description: This project's work resulted in the following research projects: (1) BORG - Block-reORGanization for Self-optimizing Storage Systems; (2) ABLE - Active Block Layer Extensions; (3) EXCES - EXternal Caching in Energy-Saving Storage Systems; (4) GRIO - Guaranteed-Rate I/O Scheduler. These projects together help in substantially advancing the over-arching project goal of developing 'QoS-Enabled, High-Performance Storage Systems'.
Date: May 31, 2009
Creator: Rangaswami, Raju
Partner: UNT Libraries Government Documents Department

Summary Report for the SINBAD Search Tool Project

Description: The Shielding Integral Benchmark Archive Database (SINBAD) Search Tool has been developed to serve as an interface with the SINBAD database to facilitate a simple and quick means of searching for information related to experimental benchmark problems. The Search Tool is written in Java and provides a better and efficient way to retrieve information from the SINBAD database. Searches can be performed quickly and easily. With regard to improvements, users are no longer required to know the name of the benchmarks to search the database. Instead, a search can be performed by specifying the experimental facility, constituents of the experimental benchmark, etc. In summary, a new powerful database search tool has been developed for SINBAD.
Date: June 1, 2012
Creator: Cunha Da Silva, Alice
Partner: UNT Libraries Government Documents Department

Smart Libraries: Best SQE Practices for Libraries with an Emphasis on Scientific Computing

Description: As scientific computing applications grow in complexity, more and more functionality is being packaged in independently developed libraries. Worse, as the computing environments in which these applications run grow in complexity, it gets easier to make mistakes in building, installing and using libraries as well as the applications that depend on them. Unfortunately, SQA standards so far developed focus primarily on applications, not libraries. We show that SQA standards for libraries differ from applications in many respects. We introduce and describe a variety of practices aimed at minimizing the likelihood of making mistakes in using libraries and at maximizing users' ability to diagnose and correct them when they occur. We introduce the term Smart Library to refer to a library that is developed with these basic principles in mind. We draw upon specific examples from existing products we believe incorporate smart features: MPI, a parallel message passing library, and HDF5 and SAF, both of which are parallel I/O libraries supporting scientific computing applications. We conclude with a narrative of some real-world experiences in using smart libraries with Ale3d, VisIt and SAF.
Date: December 15, 2004
Creator: Miller, M C; Reus, J F; Matzke, R P; Koziol, Q A & Cheng, A P
Partner: UNT Libraries Government Documents Department


Description: Chemical safety and lifecycle management (CSLM) is a process that involves managing chemicals and chemical information from the moment someone begins to order a chemical and lasts through final disposition(1). Central to CSLM is tracking data associated with chemicals which, for the purposes of this paper, is termed the chemical inventory. Examples of data that could be tracked include chemical identity, location, quantity, date procured, container type, and physical state. The reason why so much data is tracked is that the chemical inventory supports many functions. These functions include emergency management, which depends upon the data to more effectively plan for, and respond to, chemical accidents; environmental management that uses inventory information to aid in the generation of various federally-mandated and other regulatory reports; and chemical management that uses the information to increase the efficiency and safety with which chemicals are stored and utilized. All of the benefits of having an inventory are predicated upon having an inventory that is reasonably accurate. Because of the importance of ensuring one's chemical inventory is accurate, many have become concerned about measuring inventory accuracy. But beyond providing a measure of confidence in information gleaned from the inventory, does the inventory accuracy measurement provide any additional function? The answer is 'Yes'. It provides valuable information that can be used as a leading indicator to gauge the health of a chemical management system. In this paper, we will discuss: what properties make leading indicators effective, how chemical inventories can be used as a leading indicator, how chemical inventory accuracy can be measured, what levels of accuracies should realistically be expected in a healthy system, and what a subpar inventory accuracy measurement portends.
Date: February 10, 2011
Creator: Kuntamukkula, M.
Partner: UNT Libraries Government Documents Department

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

Description: SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easy access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.
Date: January 1, 2002
Creator: Starr, D. L. (Dan L.); Wozniak, P. R. (Przemyslaw R.) & Vestrand, W. T. (W. Thomas)
Partner: UNT Libraries Government Documents Department

View discovery in OLAP databases through statistical combinatorial optimization

Description: OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.
Date: January 1, 2009
Creator: Hengartner, Nick W; Burke, John; Critchlow, Terence; Joslyn, Cliff & Hogan, Emilie
Partner: UNT Libraries Government Documents Department