SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

Fermilab Security Site Access Request Database

Science.gov Websites

Fermilab Security Site Access Request Database Use of the online version of the Fermilab Security Site Access Request Database requires that you login into the ESH&Q Web Site. Note: Only Fermilab generated from the ESH&Q Section's Oracle database on May 27, 2018 05:48 AM. If you have a question

Ocean Drilling Program: Publication Services: Online Manuscript Submission

Science.gov Websites

products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP/TAMU Science Operator Home ODP's main web site Publications Policy Author Instructions Scientific Results Manuscript use the submission and review forms available on the IODP-USIO publications web site. ODP | Search

THE ECOTOX DATABASE AND ECOLOGICAL SOIL SCREENING LEVEL (ECO-SSL) WEB SITES

EPA Science Inventory

The EPA's ECOTOX database (http://www.epa.gov/ecotox/) provides a web browser search interface for locating aquatic and terrestrial toxic effects information. Data on more than 8100 chemicals and 5700 terrestrial and aquatic species are included in the database. Information is ...

Evaluation of the Content and Accessibility of Web Sites for Accredited Orthopaedic Trauma Surgery Fellowships.

PubMed

Shaath, M Kareem; Yeranosian, Michael G; Ippolito, Joseph A; Adams, Mark R; Sirkin, Michael S; Reilly, Mark C

2018-05-02

Orthopaedic trauma fellowship applicants use online-based resources when researching information on potential U.S. fellowship programs. The 2 primary sources for identifying programs are the Orthopaedic Trauma Association (OTA) database and the San Francisco Match (SF Match) database. Previous studies in other orthopaedic subspecialty areas have demonstrated considerable discrepancies among fellowship programs. The purpose of this study was to analyze content and availability of information on orthopaedic trauma surgery fellowship web sites. The online databases of the OTA and SF Match were reviewed to determine the availability of embedded program links or external links for the included programs. Thereafter, a Google search was performed for each program individually by typing the program's name, followed by the term "orthopaedic trauma fellowship." All identified fellowship web sites were analyzed for accessibility and content. Web sites were evaluated for comprehensiveness in mentioning key components of the orthopaedic trauma surgery curriculum. By consensus, we refined the final list of variables utilizing the methodology of previous studies on the topic. We identified 54 OTA-accredited fellowship programs, offering 87 positions. The majority (94%) of programs had web sites accessible through a Google search. Of the 51 web sites found, all (100%) described their program. Most commonly, hospital affiliation (88%), operative experiences (76%), and rotation overview (65%) were listed, and, least commonly, interview dates (6%), selection criteria (16%), on-call requirements (20%), and fellow evaluation criteria (20%) were listed. Programs with ≥2 fellows provided more information with regard to education content (p = 0.0001) and recruitment content (p = 0.013). Programs with Accreditation Council for Graduate Medical Education (ACGME) accreditation status also provided greater information with regard to education content (odds ratio, 4.0; p = 0.0001). Otherwise, no differences were seen by region, residency affiliation, medical school affiliation, or hospital affiliation. The SF Match and OTA databases provide few direct links to fellowship web sites. Individual program web sites do not effectively and completely convey information about the programs. The Internet is an underused resource for fellow recruitment. The lack of information on these sites allows for future opportunity to optimize this resource.

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

Globe Teachers Guide and Photographic Data on the Web

NASA Technical Reports Server (NTRS)

Kowal, Dan

2004-01-01

The task of managing the GLOBE Online Teacher s Guide during this time period focused on transforming the technology behind the delivery system of this document. The web application transformed from a flat file retrieval system to a dynamic database access approach. The new methodology utilizes Java Server Pages (JSP) on the front-end and an Oracle relational database on the backend. This new approach allows users of the web site, mainly teachers, to access content efficiently by grade level and/or by investigation or educational concept area. Moreover, teachers can gain easier access to data sheets and lab and field guides. The new online guide also included updated content for all GLOBE protocols. The GLOBE web management team was given documentation for maintaining the new application. Instructions for modifying the JSP templates and managing database content were included in this document. It was delivered to the team by the end of October, 2003. The National Geophysical Data Center (NGDC) continued to manage the school study site photos on the GLOBE website. 333 study site photo images were added to the GLOBE database and posted on the web during this same time period for 64 schools. Documentation for processing study site photos was also delivered to the new GLOBE web management team. Lastly, assistance was provided in transferring reference applications such as the Cloud and LandSat quizzes and Earth Systems Online Poster from NGDC servers to GLOBE servers along with documentation for maintaining these applications.

Getting To Know the "Invisible Web."

ERIC Educational Resources Information Center

Smith, C. Brian

2001-01-01

Discusses the portions of the World Wide Web that cannot be accessed via directories or search engines, explains why they can't be accessed, and offers suggestions for reference librarians to find these sites. Lists helpful resources and gives examples of invisible Web sites which are often databases. (LRW)

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

Public outreach and communications of the Alaska Volcano Observatory during the 2005-2006 eruption of Augustine Volcano: Chapter 27 in The 2006 eruption of Augustine Volcano, Alaska

USGS Publications Warehouse

Adleman, Jennifer N.; Cameron, Cheryl E.; Snedigar, Seth F.; Neal, Christina A.; Wallace, Kristi L.; Power, John A.; Coombs, Michelle L.; Freymueller, Jeffrey T.

2010-01-01

The AVO Web site, with its accompanying database, is the backbone of AVO's external and internal communications. This was the first Cook Inlet volcanic eruption with a public expectation of real-time access to data, updates, and hazards information over the Internet. In March 2005, AVO improved the Web site from individual static pages to a dynamic, database-driven site. This new system provided quick and straightforward access to the latest information for (1) staff within the observatory, (2) emergency managers from State and local governments and organizations, (3) the media, and (4) the public. From mid-December 2005 through April 2006, the AVO Web site served more than 45 million Web pages and about 5.5 terabytes of data.

Relational databases: a transparent framework for encouraging biology students to think informatically.

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically

PubMed Central

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. PMID:15592597

Browser-Based Online Applications: Something for Everyone!

ERIC Educational Resources Information Center

Descy, Don E.

2007-01-01

Just as many people log onto a Web mail site (Gmail, Yahoo, MSN, etc.) to read, write and store their email, there are Web sites out there with word processing, database, and a myriad of other software applications that are not downloadable but used on the site through a Web browser. The user does not have to download the applications to a…

Web Proxy Auto Discovery for the WLCG

NASA Astrophysics Data System (ADS)

Dykstra, D.; Blomer, J.; Blumenfeld, B.; De Salvo, A.; Dewhurst, A.; Verguilov, V.

2017-10-01

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily support that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which they direct to the nearest publicly accessible web proxy servers. The responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.

Web Proxy Auto Discovery for the WLCG

DOE PAGES

Dykstra, D.; Blomer, J.; Blumenfeld, B.; ...

2017-11-23

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

Web Proxy Auto Discovery for the WLCG

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

Dykstra, D.; Blomer, J.; Blumenfeld, B.

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

Web Design Matters

ERIC Educational Resources Information Center

Mathews, Brian

2009-01-01

The web site is a library's most important feature. Patrons use the web site for numerous functions, such as renewing materials, placing holds, requesting information, and accessing databases. The homepage is the place they turn to look up the hours, branch locations, policies, and events. Whether users are at work, at home, in a building, or on…

Upgrades to the TPSX Material Properties Database

NASA Technical Reports Server (NTRS)

Squire, T. H.; Milos, F. S.; Partridge, Harry (Technical Monitor)

2001-01-01

The TPSX Material Properties Database is a web-based tool that serves as a database for properties of advanced thermal protection materials. TPSX provides an easy user interface for retrieving material property information in a variety of forms, both graphical and text. The primary purpose and advantage of TPSX is to maintain a high quality source of often used thermal protection material properties in a convenient, easily accessible form, for distribution to government and aerospace industry communities. Last year a major upgrade to the TPSX web site was completed. This year, through the efforts of researchers at several NASA centers, the Office of the Chief Engineer awarded funds to update and expand the databases in TPSX. The FY01 effort focuses on updating correcting the Ames and Johnson thermal protection materials databases. In this session we will summarize the improvements made to the web site last year, report on the status of the on-going database updates, describe the planned upgrades for FY02 and FY03, and provide a demonstration of TPSX.

Ocean Drilling Program: Science Operator Search Engine

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main -USIO site, plus IODP, ODP, and DSDP Publications, together or separately. ODP | Search | Database

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

The system is developed to collect, process, store and present the information provided by the radio frequency identification (RFID) devices. The system contains three parts, the application software, the database and the web page. The application software manages multiple RFID devices, such as readers and portals, simultaneously. It communicates with the devices through application programming interface (API) provided by the device vendor. The application software converts data collected by the RFID readers and portals to readable information. It is capable of encrypting data using 256 bits advanced encryption standard (AES). The application software has a graphical user interface (GUI). Themore » GUI mimics the configurations of the nucler material storage sites or transport vehicles. The GUI gives the user and system administrator an intuitive way to read the information and/or configure the devices. The application software is capable of sending the information to a remote, dedicated and secured web and database server. Two captured screen samples, one for storage and transport, are attached. The database is constructed to handle a large number of RFID tag readers and portals. A SQL server is employed for this purpose. An XML script is used to update the database once the information is sent from the application software. The design of the web page imitates the design of the application software. The web page retrieves data from the database and presents it in different panels. The user needs a user name combined with a password to access the web page. The web page is capable of sending e-mail and text messages based on preset criteria, such as when alarm thresholds are excceeded. A captured screen sample is attached. The application software is designed to be installed on a local computer. The local computer is directly connected to the RFID devices and can be controlled locally or remotely. There are multiple local computers managing different sites or transport vehicles. The control from remote sites and information transmitted to a central database server is through secured internet. The information stored in the central databaser server is shown on the web page. The users can view the web page on the internet. A dedicated and secured web and database server (https) is used to provide information security.« less

7 CFR 3430.55 - Technical reporting.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the Current Research Information System (CRIS). (b) Initial Documentation in the CRIS Database... identification of equipment purchased with any Federal funds under the award and any subsequent use of such equipment. (e) CRIS Web Site Via Internet. The CRIS database is available to the public on the worldwide web...

Online Islamic Organizations and Measuring Web Effectiveness

DTIC Science & Technology

2004-12-01

Internet Research 13 (2003) : 17-26. Retrived from ProQuest online database on 15 May 2004. Lee, Jae-Kwan. “A model for monitoring public sector...Web site strategy.” Internet Research : Electronic Networking Applications and Policy 13 (2003) : 259-266. Retrieved from Emerad online database on

78 FR 42775 - CGI Federal, Inc., and Custom Applications Management; Transfer of Data

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-17

... develop applications, Web sites, Web pages, web-based applications and databases, in accordance with EPA policies and related Federal standards and procedures. The Contractor will provide [[Page 42776

Prototype of web-based database of surface wave investigation results for site classification

NASA Astrophysics Data System (ADS)

Hayashi, K.; Cakir, R.; Martin, A. J.; Craig, M. S.; Lorenzo, J. M.

2016-12-01

As active and passive surface wave methods are getting popular for evaluating site response of earthquake ground motion, demand on the development of database for investigation results is also increasing. Seismic ground motion not only depends on 1D velocity structure but also on 2D and 3D structures so that spatial information of S-wave velocity must be considered in ground motion prediction. The database can support to construct 2D and 3D underground models. Inversion of surface wave processing is essentially non-unique so that other information must be combined into the processing. The database of existed geophysical, geological and geotechnical investigation results can provide indispensable information to improve the accuracy and reliability of investigations. Most investigations, however, are carried out by individual organizations and investigation results are rarely stored in the unified and organized database. To study and discuss appropriate database and digital standard format for the surface wave investigations, we developed a prototype of web-based database to store observed data and processing results of surface wave investigations that we have performed at more than 400 sites in U.S. and Japan. The database was constructed on a web server using MySQL and PHP so that users can access to the database through the internet from anywhere with any device. All data is registered in the database with location and users can search geophysical data through Google Map. The database stores dispersion curves, horizontal to vertical spectral ratio and S-wave velocity profiles at each site that was saved in XML files as digital data so that user can review and reuse them. The database also stores a published 3D deep basin and crustal structure and user can refer it during the processing of surface wave data.

Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

PubMed Central

Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

2013-01-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

PubMed

Kirshner, Daniel A; Nilmeier, Jerome P; Lightstone, Felice C

2013-07-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov.

CT colonography: Project of High National Interest No. 2005062137 of the Italian Ministry of Education, University and Research (MIUR).

PubMed

Neri, E; Laghi, A; Regge, D; Sacco, P; Gallo, T; Turini, F; Talini, E; Ferrari, R; Mellaro, M; Rengo, M; Marchi, S; Caramella, D; Bartolozzi, C

2008-12-01

The aim of this paper is to describe the Web site of the Italian Project on CT Colonography (Research Project of High National Interest, PRIN No. 2005062137) and present the prototype of the online database. The Web site was created with Microsoft Office Publisher 2003 software, which allows the realisation of multiple Web pages linked through a main menu located on the home page. The Web site contains a database of computed tomography (CT) colonography studies in the Digital Imaging and Communications in Medicine (DICOM) standard, all acquired with multidetector-row CT according to the parameters defined by the European Society of Abdominal and Gastrointestinal Radiology (ESGAR). The cases present different bowel-cleansing and tagging methods, and each case has been anonymised and classified according to the Colonography Reporting and Data System (C-RADS). The Web site is available at http address www.ctcolonography.org and is composed of eight pages. Download times for a 294-Mbyte file were 33 min from a residential ADSL (6 Mbit/s) network, 200 s from a local university network (100 Mbit/s) and 2 h and 50 min from a remote academic site in the USA. The Web site received 256 accesses in the 22 days since it went online. The Web site is an immediate and up-to-date tool for publicising the activity of the research project and a valuable learning resource for CT colonography.

Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.

MAGA, a new database of gas natural emissions: a collaborative web environment for collecting data.

NASA Astrophysics Data System (ADS)

Cardellini, Carlo; Chiodini, Giovanni; Frigeri, Alessandro; Bagnato, Emanuela; Frondini, Francesco; Aiuppa, Alessandro

2014-05-01

The data on volcanic and non-volcanic gas emissions available online are, as today, are incomplete and most importantly, fragmentary. Hence, there is need for common frameworks to aggregate available data, in order to characterize and quantify the phenomena at various scales. A new and detailed web database (MAGA: MApping GAs emissions) has been developed, and recently improved, to collect data on carbon degassing form volcanic and non-volcanic environments. MAGA database allows researchers to insert data interactively and dynamically into a spatially referred relational database management system, as well as to extract data. MAGA kicked-off with the database set up and with the ingestion in to the database of the data from: i) a literature survey on publications on volcanic gas fluxes including data on active craters degassing, diffuse soil degassing and fumaroles both from dormant closed-conduit volcanoes (e.g., Vulcano, Phlegrean Fields, Santorini, Nysiros, Teide, etc.) and open-vent volcanoes (e.g., Etna, Stromboli, etc.) in the Mediterranean area and Azores, and ii) the revision and update of Googas database on non-volcanic emission of the Italian territory (Chiodini et al., 2008), in the framework of the Deep Earth Carbon Degassing (DECADE) research initiative of the Deep Carbon Observatory (DCO). For each geo-located gas emission site, the database holds images and description of the site and of the emission type (e.g., diffuse emission, plume, fumarole, etc.), gas chemical-isotopic composition (when available), gas temperature and gases fluxes magnitude. Gas sampling, analysis and flux measurement methods are also reported together with references and contacts to researchers expert of each site. In this phase data can be accessed on the network from a web interface, and data-driven web service, where software clients can request data directly from the database, are planned to be implemented shortly. This way Geographical Information Systems (GIS) and Virtual Globes (e.g., Google Earth) could easily access the database, and data could be exchanged with other database. At the moment the database includes: i) more than 1000 flux data about volcanic plume degassing from Etna and Stromboli volcanoes, ii) data from ~ 30 sites of diffuse soil degassing from Napoletan volcanoes, Azores, Canary, Etna, Stromboli, and Vulcano Island, several data on fumarolic emissions (~ 7 sites) with CO2 fluxes; iii) data from ~ 270 non volcanic gas emission site in Italy. We believe MAGA data-base is an important starting point to develop a large scale, expandable data-base aimed to excite, inspire, and encourage participation among researchers. In addition, the possibility to archive location and qualitative information for gas emission/sites not yet investigated, could stimulate the scientific community for future researches and will provide an indication on the current uncertainty on deep carbon fluxes global estimates

Using Web-based Tutorials To Enhance Library Instruction.

ERIC Educational Resources Information Center

Kocour, Bruce G.

2000-01-01

Describes the development of a Web site for library instruction at Carson-Newman College (TN) and its integration into English composition courses. Describes the use of a virtual tour, a tutorial on database searching, tutorials on specific databases, and library guides to specific disciplines to create an effective mechanism for active learning.…

CAM on PubMed

MedlinePlus

... citations from the MEDLINE database and additional life science journals. It also includes links to many full-text articles at journal Web sites and other related Web resources. Sample Searches ...

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

PubMed Central

Castagnetto, Jesus M.; Hennessy, Sean W.; Roberts, Victoria A.; Getzoff, Elizabeth D.; Tainer, John A.; Pique, Michael E.

2002-01-01

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB. PMID:11752342

Usability Testing for e-Resource Discovery: How Students Find and Choose e-Resources Using Library Web Sites

ERIC Educational Resources Information Center

Fry, Amy; Rich, Linda

2011-01-01

In early 2010, library staff at Bowling Green State University (BGSU) in Ohio designed and conducted a usability study of key parts of the library web site, focusing on the web pages generated by the library's electronic resources management system (ERM) that list and describe the library's databases. The goal was to discover how users find and…

Astronomical databases of Nikolaev Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Y.; Mazhaev, A.

2008-07-01

Several astronomical databases were created at Nikolaev Observatory during the last years. The databases are built by using MySQL search engine and PHP scripts. They are available on NAO web-site http://www.mao.nikolaev.ua.

Illinois hospital using Web to build database for relationship marketing.

PubMed

Rees, T

2000-01-01

Silver Cross Hospital and Medical Centers, Joliet, Ill., is promoting its Web site as a tool for gathering health information about patients and prospective patients in order to build a relationship marketing database. The database will enable the hospital to identify health care needs of consumers in Joliet, Will County and many southwestern suburbs of Chicago. The Web site is promoted in a multimedia advertising campaign that invites residents to participate in a Healthy Living Quiz that rewards respondents with free health screenings. The effort is part of a growing planning and marketing strategy in the health care industry called customer relationship management (CRM). Not only does a total CRM plan offer health care organizations the chance to discover the potential for meeting consumers' needs; it also helps find any marketplace gaps that may exist.

A survey of the current status of web-based databases indexing Iranian journals.

PubMed

Merat, Shahin; Khatibzadeh, Shahab; Mesgarpour, Bita; Malekzadeh, Reza

2009-05-01

The scientific output of Iran is increasing rapidly during the recent years. Unfortunately, most papers are published in journals which are not indexed by popular indexing systems and many of them are in Persian without English translation. This makes the results of Iranian scientific research unavailable to other researchers, including Iranians. The aim of this study was to evaluate the quality of current web-based databases indexing scientific articles published in Iran. We identified web-based databases which indexed scientific journals published in Iran using popular search engines. The sites were then subjected to a series of tests to evaluate their coverage, search capabilities, stability, accuracy of information, consistency, accessibility, ease of use, and other features. Results were compared with each other to identify strengths and shortcomings of each site. Five web sites were indentified. None had a complete coverage on scientific Iranian journals. The search capabilities were less than optimal in most sites. English translations of research titles, author names, keywords, and abstracts of Persian-language articles did not follow standards. Some sites did not cover abstracts. Numerous typing errors make searches ineffective and citation indexing unreliable. None of the currently available indexing sites are capable of presenting Iranian research to the international scientific community. The government should intervene by enforcing policies designed to facilitate indexing through a systematic approach. The policies should address Iranian journals, authors, and indexing sites. Iranian journals should be required to provide their indexing data, including references, electronically; authors should provide correct indexing information to journals; and indexing sites should improve their software to meet standards set by the government.

Web-Resources for Astronomical Data in the Ultraviolet

NASA Astrophysics Data System (ADS)

Sachkov, M. E.; Malkov, O. Yu.

2017-12-01

In this paper we describe databases of space projects that are operating or have operated in the ultraviolet spectral region. We give brief descriptions and links to major sources for UV data on the web: archives, space mission sites, databases, catalogues. We pay special attention to the World Space Observatory—Ultraviolet mission that will be launched in 2021.

Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1.

PubMed

Park, Jeongbin; Bae, Sangsu

2018-03-15

Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time. Free access at http://www.rgenome.net/cpf1-database/. sangsubae@hanyang.ac.kr.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins.

PubMed

Konc, Janez; Janežič, Dušanka

2017-09-01

ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis.nih.gov. Copyright © 2017 Elsevier Ltd. All rights reserved.

INFOMAT: The international materials assessment and application centre's internet gateway

NASA Astrophysics Data System (ADS)

Branquinho, Carmen Lucia; Colodete, Leandro Tavares

2004-08-01

INFOMAT is an electronic directory structured to facilitate the search and retrieval of materials science and technology information sources. Linked to the homepage of the International Materials Assessment and Application Centre, INFOMAT presents descriptions of 392 proprietary databases with links to their host systems as well as direct links to over 180 public domain databases and over 2,400 web sites. Among the web sites are associations/unions, governmental and non-governmental institutions, industries, library holdings, market statistics, news services, on-line publications, standardization and intellectual property organizations, and universities/research groups.

S/MARt DB: a database on scaffold/matrix attached regions.

PubMed

Liebich, Ines; Bode, Jürgen; Frisch, Matthias; Wingender, Edgar

2002-01-01

S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research.

Drinking Water Treatability Database (Database)

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

A Framework for Transparently Accessing Deep Web Sources

ERIC Educational Resources Information Center

Dragut, Eduard Constantin

2010-01-01

An increasing number of Web sites expose their content via query interfaces, many of them offering the same type of products/services (e.g., flight tickets, car rental/purchasing). They constitute the so-called "Deep Web". Accessing the content on the Deep Web has been a long-standing challenge for the database community. For a user interested in…

GMODWeb: a web framework for the generic model organism database

PubMed Central

O'Connor, Brian D; Day, Allen; Cain, Scott; Arnaiz, Olivier; Sperling, Linda; Stein, Lincoln D

2008-01-01

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from . PMID:18570664

Development of a web geoservices platform for School of Environmental Sciences, Mahatma Gandhi University, Kerala, India

NASA Astrophysics Data System (ADS)

Satheendran, S.; John, C. M.; Fasalul, F. K.; Aanisa, K. M.

2014-11-01

Web geoservices is the obvious graduation of Geographic Information System in a distributed environment through a simple browser. It enables organizations to share domain-specific rich and dynamic spatial information over the web. The present study attempted to design and develop a web enabled GIS application for the School of Environmental Sciences, Mahatma Gandhi University, Kottayam, Kerala, India to publish various geographical databases to the public through its website. The development of this project is based upon the open source tools and techniques. The output portal site is platform independent. The premier webgis frame work `Geomoose' is utilized. Apache server is used as the Web Server and the UMN Map Server is used as the map server for this project. It provides various customised tools to query the geographical database in different ways and search for various facilities in the geographical area like banks, attractive places, hospitals, hotels etc. The portal site was tested with the output geographical database of 2 projects of the School such as 1) the Tourism Information System for the Malabar region of Kerala State consisting of 5 northern districts 2) the geoenvironmental appraisal of the Athirappilly Hydroelectric Project covering the entire Chalakkudy river basin.

The development of a new database of gas emissions: MAGA, a collaborative web environment for collecting data

NASA Astrophysics Data System (ADS)

Cardellini, C.; Chiodini, G.; Frigeri, A.; Bagnato, E.; Aiuppa, A.; McCormick, B.

2013-12-01

The data on volcanic and non-volcanic gas emissions available online are, as today, incomplete and most importantly, fragmentary. Hence, there is need for common frameworks to aggregate available data, in order to characterize and quantify the phenomena at various spatial and temporal scales. Building on the Googas experience we are now extending its capability, particularly on the user side, by developing a new web environment for collecting and publishing data. We have started to create a new and detailed web database (MAGA: MApping GAs emissions) for the deep carbon degassing in the Mediterranean area. This project is part of the Deep Earth Carbon Degassing (DECADE) research initiative, lunched in 2012 by the Deep Carbon Observatory (DCO) to improve the global budget of endogenous carbon from volcanoes. MAGA database is planned to complement and integrate the work in progress within DECADE in developing CARD (Carbon Degassing) database. MAGA database will allow researchers to insert data interactively and dynamically into a spatially referred relational database management system, as well as to extract data. MAGA kicked-off with the database set up and a complete literature survey on publications on volcanic gas fluxes, by including data on active craters degassing, diffuse soil degassing and fumaroles both from dormant closed-conduit volcanoes (e.g., Vulcano, Phlegrean Fields, Santorini, Nysiros, Teide, etc.) and open-vent volcanoes (e.g., Etna, Stromboli, etc.) in the Mediterranean area and Azores. For each geo-located gas emission site, the database holds images and description of the site and of the emission type (e.g., diffuse emission, plume, fumarole, etc.), gas chemical-isotopic composition (when available), gas temperature and gases fluxes magnitude. Gas sampling, analysis and flux measurement methods are also reported together with references and contacts to researchers expert of the site. Data can be accessed on the network from a web interface or as a data-driven web service, where software clients can request data directly from the database. This way Geographical Information Systems (GIS) and Virtual Globes (e.g., Google Earth) can easily access the database, and data can be exchanged with other database. In details the database now includes: i) more than 1000 flux data about volcanic plume degassing from Etna (4 summit craters and bulk degassing) and Stromboli volcanoes, with time averaged CO2 fluxes of ~ 18000 and 766 t/d, respectively; ii) data from ~ 30 sites of diffuse soil degassing from Napoletan volcanoes, Azores, Canary, Etna, Stromboli, and Vulcano Island, with a wide range of CO2 fluxes (from les than 1 to 1500 t/d) and iii) several data on fumarolic emissions (~ 7 sites) with CO2 fluxes up to 1340 t/day (i.e., Stromboli). When available, time series of compositional data have been archived in the database (e.g., for Campi Flegrei fumaroles). We believe MAGA data-base is an important starting point to develop a large scale, expandable data-base aimed to excite, inspire, and encourage participation among researchers. In addition, the possibility to archive location and qualitative information for gas emission/sites not yet investigated, could stimulate the scientific community for future researches and will provide an indication on the current uncertainty on deep carbon fluxes global estimates.

Global Access to Library of Congress' Digital Resources: National Digital Library and Internet Resources.

ERIC Educational Resources Information Center

Chen, Ching-chih

1996-01-01

Summarizes how the Library of Congress' digital library collections can be accessed globally via the Internet and World Wide Web. Outlines the resources found in each of the various access points: gopher, online catalog, library and legislative Web sites, legal and copyright databases, and FTP (file transfer protocol) sites. (LAM)

Ocean Drilling Program: Mirror Sites

Science.gov Websites

Publication services and products Drilling services and tools Online Janus database Search the ODP/TAMU web information, see www.iodp-usio.org. ODP | Search | Database | Drilling | Publications | Science | Cruise Info

Massage Therapy for Health Purposes

MedlinePlus

... Web site: www.nih.gov/health/clinicaltrials/ Cochrane Database of Systematic Reviews The Cochrane Database of Systematic ... Licensed Complementary and Alternative Healthcare Professions. Seattle, WA: Academic Consortium for Complementary and Alternative Health Care; 2009. ...

Hot Topics on the Web: Strategies for Research.

ERIC Educational Resources Information Center

Diaz, Karen R.; O'Hanlon, Nancy

2001-01-01

Presents strategies for researching topics on the Web that are controversial or current in nature. Discusses topic selection and overviews, including the use of online encyclopedias; search engines; finding laws and pending legislation; advocacy groups; proprietary databases; Web site evaluation; and the continuing usefulness of print materials.…

The Implications of Well-Formedness on Web-Based Educational Resources.

ERIC Educational Resources Information Center

Mohler, James L.

Within all institutions, Web developers are beginning to utilize technologies that make sites more than static information resources. Databases such as XML (Extensible Markup Language) and XSL (Extensible Stylesheet Language) are key technologies that promise to extend the Web beyond the "information storehouse" paradigm and provide…

Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

PubMed

Condie, Brian G; Urbanski, William M

2014-01-01

Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

75 FR 28024 - Agency Information Collection Activities: Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-19

... the data-capturing process. SAMHSA will place Web site registration information into a Knowledge Management database and will place email subscription information into a database maintained by a third-party...

Web impact factor: a bibliometric criterion applied to medical informatics societies' web sites.

PubMed

Soualmia, Lina Fatima; Darmoni, Stéfan Jacques; Le Duff, Franck; Douyere, Magaly; Thelwall, Maurice

2002-01-01

Several methods are available to evaluate and compare medical journals. The most popular is the journal Impact Factor, derived from averaging counts of citations to articles. Ingwersen adapted this method to assess the attractiveness of Web sites, defining the external Web Impact Factor (WIF) to be the number of external pages containing a link to a given Web site. This paper applies the WIF to 43 medical informatics societies' Web sites using advanced search engine queries to obtain the necessary link counts. The WIF was compared to the number of publications available in the Medline bibliographic database in medical informatics in these 43 countries. Between these two metrics, the observed Pearson correlation was 0.952 (p < 0.01) and the Spearman rank correlation was 0.548 (p < 0.01) showing in both cases a positive and strong significant correlation. The WIF of medicalm informatics society's Web site is statistically related to national productivity and discrepancies can be used to indicate countries where there are either weak medical informatics associations, or ones that do not make optimal use of the Web.

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

Access to Space Interactive Design Web Site

NASA Technical Reports Server (NTRS)

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

The Innate Immune Database (IIDB)

PubMed Central

Korb, Martin; Rust, Aistair G; Thorsson, Vesteinn; Battail, Christophe; Li, Bin; Hwang, Daehee; Kennedy, Kathleen A; Roach, Jared C; Rosenberger, Carrie M; Gilchrist, Mark; Zak, Daniel; Johnson, Carrie; Marzolf, Bruz; Aderem, Alan; Shmulevich, Ilya; Bolouri, Hamid

2008-01-01

Background As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site . Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens. Description We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser. Conclusion We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at . PMID:18321385

Image

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

Marsh, Amber; Harsch, Tim; Pitt, Julie

2007-08-31

The computer side of the IMAGE project consists of a collection of Perl scripts that perform a variety of tasks; scripts are available to insert, update and delete data from the underlying Oracle database, download data from NCBI's Genbank and other sources, and generate data files for download by interested parties. Web scripts make up the tracking interface, and various tools available on the project web-site (image.llnl.gov) that provide a search interface to the database.

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2012 CFR

2012-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

A Web-based tool for UV irradiance data: predictions for European and Southeast Asian sites.

PubMed

Kift, Richard; Webb, Ann R; Page, John; Rimmer, John; Janjai, Serm

2006-01-01

There are a range of UV models available, but one needs significant pre-existing knowledge and experience in order to be able to use them. In this article a comparatively simple Web-based model developed for the SoDa (Integration and Exploitation of Networked Solar Radiation Databases for Environment Monitoring) project is presented. This is a clear-sky model with modifications for cloud effects. To determine if the model produces realistic UV data the output is compared with 1 year sets of hourly measurements at sites in the United Kingdom and Thailand. The accuracy of the output depends on the input, but reasonable results were obtained with the use of the default database inputs and improved when pyranometer instead of modeled data provided the global radiation input needed to estimate the UV. The average modeled values of UV for the UK site were found to be within 10% of measurements. For the tropical sites in Thailand the average modeled values were within 1120% of measurements for the four sites with the use of the default SoDa database values. These results improved when pyranometer data and TOMS ozone data from 2002 replaced the standard SoDa database values, reducing the error range for all four sites to less than 15%.

Web-based X-ray quality control documentation.

PubMed

David, George; Burnett, Lou Ann; Schenkel, Robert

2003-01-01

The department of radiology at the Medical College of Georgia Hospital and Clinics has developed an equipment quality control web site. Our goal is to provide immediate access to virtually all medical physics survey data. The web site is designed to assist equipment engineers, department management and technologists. By improving communications and access to equipment documentation, we believe productivity is enhanced. The creation of the quality control web site was accomplished in three distinct steps. First, survey data had to be placed in a computer format. The second step was to convert these various computer files to a format supported by commercial web browsers. Third, a comprehensive home page had to be designed to provide convenient access to the multitude of surveys done in the various x-ray rooms. Because we had spent years previously fine-tuning the computerization of the medical physics quality control program, most survey documentation was already in spreadsheet or database format. A major technical decision was the method of conversion of survey spreadsheet and database files into documentation appropriate for the web. After an unsatisfactory experience with a HyperText Markup Language (HTML) converter (packaged with spreadsheet and database software), we tried creating Portable Document Format (PDF) files using Adobe Acrobat software. This process preserves the original formatting of the document and takes no longer than conventional printing; therefore, it has been very successful. Although the PDF file generated by Adobe Acrobat is a proprietary format, it can be displayed through a conventional web browser using the freely distributed Adobe Acrobat Reader program that is available for virtually all platforms. Once a user installs the software, it is automatically invoked by the web browser whenever the user follows a link to a file with a PDF extension. Although no confidential patient information is available on the web site, our legal department recommended that we secure the site in order to keep out those wishing to make mischief. Our interim solution has not been to password protect the page, which we feared would hinder access for occasional legitimate users, but also not to provide links to it from other hospital and department pages. Utility and productivity were improved and time and money were saved by making radiological equipment quality control documentation instantly available on-line.

Ridge 2000 Data Management System

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Carbotte, S. M.; Arko, R. A.; Haxby, W. F.; Ryan, W. B.; Chayes, D. N.; Lehnert, K. A.; Shank, T. M.

2005-12-01

Hosted at Lamont by the marine geoscience Data Management group, mgDMS, the NSF-funded Ridge 2000 electronic database, http://www.marine-geo.org/ridge2000/, is a key component of the Ridge 2000 multi-disciplinary program. The database covers each of the three Ridge 2000 Integrated Study Sites: Endeavour Segment, Lau Basin, and 8-11N Segment. It promotes the sharing of information to the broader community, facilitates integration of the suite of information collected at each study site, and enables comparisons between sites. The Ridge 2000 data system provides easy web access to a relational database that is built around a catalogue of cruise metadata. Any web browser can be used to perform a versatile text-based search which returns basic cruise and submersible dive information, sample and data inventories, navigation, and other relevant metadata such as shipboard personnel and links to NSF program awards. In addition, non-proprietary data files, images, and derived products which are hosted locally or in national repositories, as well as science and technical reports, can be freely downloaded. On the Ridge 2000 database page, our Data Link allows users to search the database using a broad range of parameters including data type, cruise ID, chief scientist, geographical location. The first Ridge 2000 field programs sailed in 2004 and, in addition to numerous data sets collected prior to the Ridge 2000 program, the database currently contains information on fifteen Ridge 2000-funded cruises and almost sixty Alvin dives. Track lines can be viewed using a recently- implemented Web Map Service button labelled Map View. The Ridge 2000 database is fully integrated with databases hosted by the mgDMS group for MARGINS and the Antarctic multibeam and seismic reflection data initiatives. Links are provided to partner databases including PetDB, SIOExplorer, and the ODP Janus system. Improved inter-operability with existing and new partner repositories continues to be strengthened. One major effort involves the gradual unification of the metadata across these partner databases. Standardised electronic metadata forms that can be filled in at sea are available from our web site. Interactive map-based exploration and visualisation of the Ridge 2000 database is provided by GeoMapApp, a freely-available Java(tm) application being developed within the mgDMS group. GeoMapApp includes high-resolution bathymetric grids for the 8-11N EPR segment and allows customised maps and grids for any of the Ridge 2000 ISS to be created. Vent and instrument locations can be plotted and saved as images, and Alvin dive photos are also available.

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

PubMed

Miao, Zhichao; Westhof, Eric

2016-07-08

RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The New Face of FLUXNET: Redesigning the Web Site and Data Organization to Enhance the User Experience

NASA Astrophysics Data System (ADS)

Shanafield, Harold; Shamblin, Stephanie; Devarakonda, Ranjeet; McMurry, Ben; Walker Beaty, Tammy; Wilson, Bruce; Cook, Robert B.

2011-02-01

The FLUXNET global network of regional flux tower networks serves to coordinate the regional and global analysis of eddy covariance based CO2, water vapor and energy flux measurements taken at more than 500 sites in continuous long-term operation. The FLUXNET database presently contains information about the location, characteristics, and data availability of each of these sites. To facilitate the coordination and distribution of this information, we redesigned the underlying database and associated web site. We chose the PostgreSQL database as a platform based on its performance, stability and GIS extensions. PostreSQL allows us to enhance our search and presentation capabilities, which will in turn provide increased functionality for users seeking to understand the FLUXNET data. The redesigned database will also significantly decrease the burden of managing such highly varied data. The website is being developed using the Drupal content management system, which provides many community-developed modules and a robust framework for custom feature development. In parallel, we are working with the regional networks to ensure that the information in the FLUXNET database is identical to that in the regional networks. Going forward, we also plan to develop an automated way to synchronize information with the regional networks.

Science and Technology Undergraduate Students' Use of the Internet, Cell Phones and Social Networking Sites to Access Library Information

ERIC Educational Resources Information Center

Salisbury, Lutishoor; Laincz, Jozef; Smith, Jeremy J.

2012-01-01

Many academic libraries and publishers have developed mobile-optimized versions of their web sites and catalogs. Almost all database vendors and major journal publishers have provided a way to connect to their resources via the Internet and the mobile web. In light of this pervasive use of the Internet, mobile devices and social networking, this…

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

A comparative study of six European databases of medically oriented Web resources.

PubMed

Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

2005-10-01

The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

Online research databases and journals of Chinese medicine.

PubMed

Fan, Ka Wai

2004-12-01

This paper introduces journals and other research resources about Chinese medicine available online. Web sites are categorized under four headings: databases, comprehensive journals, acupuncture journals, and history and philosophy of Chinese medicine. It may assist interested people in furthering their studies.

THE DRINKING WATER TREATABILITY DATABASE (Slides)

EPA Science Inventory

The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

OriDB, the DNA replication origin database updated and extended.

PubMed

Siow, Cheuk C; Nieduszynska, Sian R; Müller, Carolin A; Nieduszynski, Conrad A

2012-01-01

OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original database collated and curated Saccharomyces cerevisiae origin mapping studies. Here, we report that the OriDB database and web site have been revamped to improve user accessibility to curated data sets, to greatly increase the number of curated origin mapping studies, and to include the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe. The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at http://cerevisiae.oridb.org/ and for S. pombe at http://pombe.oridb.org/.

Use of the World Wide Web for multisite data collection.

PubMed

Subramanian, A K; McAfee, A T; Getzinger, J P

1997-08-01

As access to the Internet becomes increasingly available, research applications in medicine will increase. This paper describes the use of the Internet, and, more specifically, the World Wide Web (WWW), as a channel of communication between EDs throughout the world and investigators who are interested in facilitating the collection of data from multiple sites. Data entered into user-friendly electronic surveys can be transmitted over the Internet to a database located at the site of the study, rendering geographic separation less of a barrier to the conduction of multisite studies. The electronic format of the data can enable real-time statistical processing while data are stored using existing database technologies. In theory, automated processing of variables within such a database enables early identification of data trends. Methods of ensuring validity, security, and compliance are discussed.

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Software Update.

ERIC Educational Resources Information Center

Currents, 2000

2000-01-01

A chart of 40 alumni-development database systems provides information on vendor/Web site, address, contact/phone, software name, price range, minimum suggested workstation/suggested server, standard reports/reporting tools, minimum/maximum record capacity, and number of installed sites/client type. (DB)

THE DRINKING WATER TREATABILITY DATABASE (Conference Paper)

EPA Science Inventory

The Drinking Water Treatability Database (TDB) assembles referenced data on the control of contaminants in drinking water, housed on an interactive, publicly-available, USEPA web site (www.epa.gov/tdb). The TDB is of use to drinking water utilities, treatment process design engin...

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

DOE PAGES

Zerkin, V. V.; Pritychenko, B.

2018-02-04

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

NASA Astrophysics Data System (ADS)

Zerkin, V. V.; Pritychenko, B.

2018-04-01

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ∼22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. It is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

Barg, M. I.; Stobie, E. B.; Ferro, A. J.; O'Neil, E. J.

In the spring of 2000, at the request of the ADASS Program Organizing Committee (POC), we began organizing information from previous ADASS conferences in an effort to create a centralized database. The beginnings of this database originated from data (invited speakers, participants, papers, etc.) extracted from HyperText Markup Language (HTML) documents from past ADASS host sites. Unfortunately, not all HTML documents are well formed and parsing them proved to be an iterative process. It was evident at the beginning that if these Web documents were organized in a standardized way, such as XML (Extensible Markup Language), the processing of this information across the Web could be automated, more efficient, and less error prone. This paper will briefly review the many programming tools available for processing XML, including Java, Perl and Python, and will explore the mapping of relational data from our MySQL database to XML.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

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

Zerkin, V. V.; Pritychenko, B.

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

Accredited hand surgery fellowship Web sites: analysis of content and accessibility.

PubMed

Trehan, Samir K; Morrell, Nathan T; Akelman, Edward

2015-04-01

To assess the accessibility and content of accredited hand surgery fellowship Web sites. A list of all accredited hand surgery fellowships was obtained from the online database of the American Society for Surgery of the Hand (ASSH). Fellowship program information on the ASSH Web site was recorded. All fellowship program Web sites were located via Google search. Fellowship program Web sites were analyzed for accessibility and content in 3 domains: program overview, application information/recruitment, and education. At the time of this study, there were 81 accredited hand surgery fellowships with 169 available positions. Thirty of 81 programs (37%) had a functional link on the ASSH online hand surgery fellowship directory; however, Google search identified 78 Web sites. Three programs did not have a Web site. Analysis of content revealed that most Web sites contained contact information, whereas information regarding the anticipated clinical, research, and educational experiences during fellowship was less often present. Furthermore, information regarding past and present fellows, salary, application process/requirements, call responsibilities, and case volume was frequently lacking. Overall, 52 of 81 programs (64%) had the minimal online information required for residents to independently complete the fellowship application process. Hand fellowship program Web sites could be accessed either via the ASSH online directory or Google search, except for 3 programs that did not have Web sites. Although most fellowship program Web sites contained contact information, other content such as application information/recruitment and education, was less frequently present. This study provides comparative data regarding the clinical and educational experiences outlined on hand fellowship program Web sites that are of relevance to residents, fellows, and academic hand surgeons. This study also draws attention to various ways in which the hand surgery fellowship application process can be made more user-friendly and efficient. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.

PubMed

Konc, Janez; Janezic, Dusanka

2012-07-01

The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si.

Ultrabroadband photonic internet: safety aspects

NASA Astrophysics Data System (ADS)

Kalicki, Arkadiusz; Romaniuk, Ryszard

2008-11-01

Web applications became most popular medium in the Internet. Popularity, easiness of web application frameworks together with careless development results in high number of vulnerabilities and attacks. There are several types of attacks possible because of improper input validation. SQL injection is ability to execute arbitrary SQL queries in a database through an existing application. Cross-site scripting is the vulnerability which allows malicious web users to inject code into the web pages viewed by other users. Cross-Site Request Forgery (CSRF) is an attack that tricks the victim into loading a page that contains malicious request. Web spam in blogs. There are several techniques to mitigate attacks. Most important are web application strong design, correct input validation, defined data types for each field and parameterized statements in SQL queries. Server hardening with firewall, modern security policies systems and safe web framework interpreter configuration are essential. It is advised to keep proper security level on client side, keep updated software and install personal web firewalls or IDS/IPS systems. Good habits are logging out from services just after finishing work and using even separate web browser for most important sites, like e-banking.

ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins

PubMed Central

Konc, Janez; Janežič, Dušanka

2012-01-01

The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si. PMID:22600737

A Grid job monitoring system

NASA Astrophysics Data System (ADS)

Dumitrescu, Catalin; Nowack, Andreas; Padhi, Sanjay; Sarkar, Subir

2010-04-01

This paper presents a web-based Job Monitoring framework for individual Grid sites that allows users to follow in detail their jobs in quasi-real time. The framework consists of several independent components : (a) a set of sensors that run on the site CE and worker nodes and update a database, (b) a simple yet extensible web services framework and (c) an Ajax powered web interface having a look-and-feel and control similar to a desktop application. The monitoring framework supports LSF, Condor and PBS-like batch systems. This is one of the first monitoring systems where an X.509 authenticated web interface can be seamlessly accessed by both end-users and site administrators. While a site administrator has access to all the possible information, a user can only view the jobs for the Virtual Organizations (VO) he/she is a part of. The monitoring framework design supports several possible deployment scenarios. For a site running a supported batch system, the system may be deployed as a whole, or existing site sensors can be adapted and reused with the web services components. A site may even prefer to build the web server independently and choose to use only the Ajax powered web interface. Finally, the system is being used to monitor a glideinWMS instance. This broadens the scope significantly, allowing it to monitor jobs over multiple sites.

Web based aphasia test using service oriented architecture (SOA)

NASA Astrophysics Data System (ADS)

Voos, J. A.; Vigliecca, N. S.; Gonzalez, E. A.

2007-11-01

Based on an aphasia test for Spanish speakers which analyze the patient's basic resources of verbal communication, a web-enabled software was developed to automate its execution. A clinical database was designed as a complement, in order to evaluate the antecedents (risk factors, pharmacological and medical backgrounds, neurological or psychiatric symptoms, brain injury -anatomical and physiological characteristics, etc) which are necessary to carry out a multi-factor statistical analysis in different samples of patients. The automated test was developed following service oriented architecture and implemented in a web site which contains a tests suite, which would allow both integrating the aphasia test with other neuropsychological instruments and increasing the available site information for scientific research. The test design, the database and the study of its psychometric properties (validity, reliability and objectivity) were made in conjunction with neuropsychological researchers, who participate actively in the software design, based on the patients or other subjects of investigation feedback.

76 FR 42677 - Notice of Intent To Seek Approval To Collect Information

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-19

... and maintains an on-line recipe database, the Recipe Finder, as a popular feature to the SNAP-Ed Connection Web site. The purpose of the Recipe Finder database is to provide SNAP-Ed providers with low-cost... inclusion in the database. SNAP-Ed staff and providers benefit from collecting and posting feedback on...

Footprint Database and web services for the Herschel space observatory

NASA Astrophysics Data System (ADS)

Verebélyi, Erika; Dobos, László; Kiss, Csaba

2015-08-01

Using all telemetry and observational meta-data, we created a searchable database of Herschel observation footprints. Data from the Herschel space observatory is freely available for everyone but no uniformly processed catalog of all observations has been published yet. As a first step, we unified the data model for all three Herschel instruments in all observation modes and compiled a database of sky coverage information. As opposed to methods using a pixellation of the sphere, in our database, sky coverage is stored in exact geometric form allowing for precise area calculations. Indexing of the footprints allows for very fast search among observations based on pointing, time, sky coverage overlap and meta-data. This enables us, for example, to find moving objects easily in Herschel fields. The database is accessible via a web site and also as a set of REST web service functions which makes it usable from program clients like Python or IDL scripts. Data is available in various formats including Virtual Observatory standards.

Evaluation of personal digital assistant drug information databases for the managed care pharmacist.

PubMed

Lowry, Colleen M; Kostka-Rokosz, Maria D; McCloskey, William W

2003-01-01

Personal digital assistants (PDAs) are becoming a necessity for practicing pharmacists. They offer a time-saving and convenient way to obtain current drug information. Several software companies now offer general drug information databases for use on hand held computers. PDAs priced less than 200 US dollars often have limited memory capacity; therefore, the user must choose from a growing list of general drug information database options in order to maximize utility without exceeding memory capacity. This paper reviews the attributes of available general drug information software databases for the PDA. It provides information on the content, advantages, limitations, pricing, memory requirements, and accessibility of drug information software databases. Ten drug information databases were subjectively analyzed and evaluated based on information from the product.s Web site, vendor Web sites, and from our experience. Some of these databases have attractive auxiliary features such as kinetics calculators, disease references, drug-drug and drug-herb interaction tools, and clinical guidelines, which may make them more useful to the PDA user. Not all drug information databases are equal with regard to content, author credentials, frequency of updates, and memory requirements. The user must therefore evaluate databases for completeness, currency, and cost effectiveness before purchase. In addition, consideration should be given to the ease of use and flexibility of individual programs.

Mining Longitudinal Web Queries: Trends and Patterns.

ERIC Educational Resources Information Center

Wang, Peiling; Berry, Michael W.; Yang, Yiheng

2003-01-01

Analyzed user queries submitted to an academic Web site during a four-year period, using a relational database, to examine users' query behavior, to identify problems they encounter, and to develop techniques for optimizing query analysis and mining. Linguistic analyses focus on query structures, lexicon, and word associations using statistical…

Cyberspace as a Theater of Conflict: Federal Law, National Strategy and the Departments of Defense and Homeland Security

DTIC Science & Technology

2007-06-01

short period of time. When web search organizations canvas the web looking for sites to catalog, they will discover your systems and create registry... Fingerprint & DNA Databases, INTERPOL & National Law Enforcement Communication Systems, Firearms Registration Records, Drivers License, Birth

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

PubMed

Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

2017-07-03

Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Explore Arctic Health.

PubMed

Lebow, Mahria

2014-04-01

The Arctic Health web site is a portal to Arctic-specific, health related content. The site provides expertly organized and annotated resources pertinent to northern peoples and places, including health information, research publications and environmental information. This site also features the Arctic Health Publications Database, which indexes an array of Arctic-related resources.

Tripal: a construction toolkit for online genome databases.

PubMed

Ficklin, Stephen P; Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net.

Tripal: a construction toolkit for online genome databases

PubMed Central

Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E.; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E.; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net PMID:21959868

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

CHIP Demonstrator: Semantics-Driven Recommendations and Museum Tour Generation

NASA Astrophysics Data System (ADS)

Aroyo, Lora; Stash, Natalia; Wang, Yiwen; Gorgels, Peter; Rutledge, Lloyd

The main objective of the CHIP project is to demonstrate how Semantic Web technologies can be deployed to provide personalized access to digital museum collections. We illustrate our approach with the digital database ARIA of the Rijksmuseum Amsterdam. For the semantic enrichment of the Rijksmuseum ARIA database we collaborated with the CATCH STITCH project to produce mappings to Iconclass, and with the MultimediaN E-culture project to produce the RDF/OWL of the ARIA and Adlib databases. The main focus of CHIP is on exploring the potential of applying adaptation techniques to provide personalized experience for the museum visitors both on the Web site and in the museum.

MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

PubMed

Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele; Andreini, Claudia

2014-08-01

We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.

Multiple-Feature Extracting Modules Based Leak Mining System Design

PubMed Central

Cho, Ying-Chiang; Pan, Jen-Yi

2013-01-01

Over the years, human dependence on the Internet has increased dramatically. A large amount of information is placed on the Internet and retrieved from it daily, which makes web security in terms of online information a major concern. In recent years, the most problematic issues in web security have been e-mail address leakage and SQL injection attacks. There are many possible causes of information leakage, such as inadequate precautions during the programming process, which lead to the leakage of e-mail addresses entered online or insufficient protection of database information, a loophole that enables malicious users to steal online content. In this paper, we implement a crawler mining system that is equipped with SQL injection vulnerability detection, by means of an algorithm developed for the web crawler. In addition, we analyze portal sites of the governments of various countries or regions in order to investigate the information leaking status of each site. Subsequently, we analyze the database structure and content of each site, using the data collected. Thus, we make use of practical verification in order to focus on information security and privacy through black-box testing. PMID:24453892

Multiple-feature extracting modules based leak mining system design.

PubMed

Cho, Ying-Chiang; Pan, Jen-Yi

2013-01-01

Over the years, human dependence on the Internet has increased dramatically. A large amount of information is placed on the Internet and retrieved from it daily, which makes web security in terms of online information a major concern. In recent years, the most problematic issues in web security have been e-mail address leakage and SQL injection attacks. There are many possible causes of information leakage, such as inadequate precautions during the programming process, which lead to the leakage of e-mail addresses entered online or insufficient protection of database information, a loophole that enables malicious users to steal online content. In this paper, we implement a crawler mining system that is equipped with SQL injection vulnerability detection, by means of an algorithm developed for the web crawler. In addition, we analyze portal sites of the governments of various countries or regions in order to investigate the information leaking status of each site. Subsequently, we analyze the database structure and content of each site, using the data collected. Thus, we make use of practical verification in order to focus on information security and privacy through black-box testing.

Analysis Tool Web Services from the EMBL-EBI.

PubMed

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

Tags Help Make Libraries Del.icio.us: Social Bookmarking and Tagging Boost Participation

ERIC Educational Resources Information Center

Rethlefsen, Melissa L.

2007-01-01

Traditional library web products, whether online public access catalogs, library databases, or even library web sites, have long been rigidly controlled and difficult to use. Patrons regularly prefer Google's simple interface. Now social bookmarking and tagging tools help librarians bridge the gap between the library's need to offer authoritative,…

48 CFR 252.204-7007 - Alternate A, Annual Representations and Certifications.

Code of Federal Regulations, 2013 CFR

2013-10-01

... for Award Management (SAM) database are applicable to this solicitation as indicated: (i) 252.209-7001... education. (iii) 252.216-7008, Economic Price Adjustment—Wage Rates or Material Prices Controlled by a... SAM Web site at https://www.acquisition.gov/. After reviewing the ORCA database information, the...

75 FR 61761 - Renewal of Charter for the Chronic Fatigue Syndrome Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-06

... professionals, and the biomedical, academic, and research communities about chronic fatigue syndrome advances... accessing the FACA database that is maintained by the Committee Management Secretariat under the General Services Administration. The Web site address for the FACA database is http://fido.gov/facadatabase . Dated...

Conducting a Web Search.

ERIC Educational Resources Information Center

Miller-Whitehead, Marie

Keyword and text string searches of online library catalogs often provide different results according to library and database used and depending upon how books and journals are indexed. For this reason, online databases such as ERIC often provide tutorials and recommendations for searching their site, such as how to use Boolean search strategies.…

Role of a database-driven web site in the immediate disaster response and recovery of Academic Health Center: the Katrina experience.

PubMed

Fordis, Michael; Alexander, J Douglas; McKellar, Julie

2007-08-01

In the wake of Hurricane Katrina's landfall on August 29, 2005, and the subsequent levee failures, operations of Tulane University School of Medicine became unsustainable. As New Orleans collapsed, faculty, students, residents, and staff were scattered nationwide. In response, four Texas medical schools created an alliance to assist Tulane in temporarily relocating operations to south Texas. Resuming operations in a three- to four-week time span required developing and implementing a coordinated communication plan in the face of widespread communication infrastructure disruptions. A keystone of the strategy involved rapidly creating a "recovery Web site" to provide essential information on immediate recovery plans, mechanisms for reestablishing communications with displaced persons, housing relocation options (over 200 students, faculty, and staff were relocated using Web site resources), classes and residency training, and other issues (e.g., financial services, counseling support) vitally important to affected individuals. The database-driven Web site was launched in four days on September 11, 2005, by modifying an existing system and completing new programming. Additional functions were added during the next week, and the site operated continuously until March 2006, providing about 890,000 pages of information in over 100,000 visitor sessions. The site proved essential in disseminating announcements, reestablishing communications among the Tulane family, and supporting relocation and recovery. This experience shows the importance of information technology in collaborative efforts of academic health centers in early disaster response and recovery, reinforcing recommendations published recently by the Association of Academic Health Centers and the National Academy of Sciences.

EVpedia: a community web portal for extracellular vesicles research.

PubMed

Kim, Dae-Kyum; Lee, Jaewook; Kim, Sae Rom; Choi, Dong-Sic; Yoon, Yae Jin; Kim, Ji Hyun; Go, Gyeongyun; Nhung, Dinh; Hong, Kahye; Jang, Su Chul; Kim, Si-Hyun; Park, Kyong-Su; Kim, Oh Youn; Park, Hyun Taek; Seo, Ji Hye; Aikawa, Elena; Baj-Krzyworzeka, Monika; van Balkom, Bas W M; Belting, Mattias; Blanc, Lionel; Bond, Vincent; Bongiovanni, Antonella; Borràs, Francesc E; Buée, Luc; Buzás, Edit I; Cheng, Lesley; Clayton, Aled; Cocucci, Emanuele; Dela Cruz, Charles S; Desiderio, Dominic M; Di Vizio, Dolores; Ekström, Karin; Falcon-Perez, Juan M; Gardiner, Chris; Giebel, Bernd; Greening, David W; Gross, Julia Christina; Gupta, Dwijendra; Hendrix, An; Hill, Andrew F; Hill, Michelle M; Nolte-'t Hoen, Esther; Hwang, Do Won; Inal, Jameel; Jagannadham, Medicharla V; Jayachandran, Muthuvel; Jee, Young-Koo; Jørgensen, Malene; Kim, Kwang Pyo; Kim, Yoon-Keun; Kislinger, Thomas; Lässer, Cecilia; Lee, Dong Soo; Lee, Hakmo; van Leeuwen, Johannes; Lener, Thomas; Liu, Ming-Lin; Lötvall, Jan; Marcilla, Antonio; Mathivanan, Suresh; Möller, Andreas; Morhayim, Jess; Mullier, François; Nazarenko, Irina; Nieuwland, Rienk; Nunes, Diana N; Pang, Ken; Park, Jaesung; Patel, Tushar; Pocsfalvi, Gabriella; Del Portillo, Hernando; Putz, Ulrich; Ramirez, Marcel I; Rodrigues, Marcio L; Roh, Tae-Young; Royo, Felix; Sahoo, Susmita; Schiffelers, Raymond; Sharma, Shivani; Siljander, Pia; Simpson, Richard J; Soekmadji, Carolina; Stahl, Philip; Stensballe, Allan; Stępień, Ewa; Tahara, Hidetoshi; Trummer, Arne; Valadi, Hadi; Vella, Laura J; Wai, Sun Nyunt; Witwer, Kenneth; Yáñez-Mó, María; Youn, Hyewon; Zeidler, Reinhard; Gho, Yong Song

2015-03-15

Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Lessons Learned Implementing DOORS in a Citrix Environment

NASA Technical Reports Server (NTRS)

Bussman, Marie

2005-01-01

NASA's James Web Space Telescope (JWST) Project is a large multi-national project with geographically dispersed contractors that all need access to the Projects requirement database. Initially, the project utilized multiple DOORS databases with the built-in partitions feature to exchange modules amongst the various contractor sites. As the requirements databases matured the use of partitions became extremely difficult. There have been many issues such as incompatible versions of DOORS, inefficient mechanism for sharing modules, security concerns, performance issues, and inconsistent document import and export formats. Deployment of the client software with limited IT resources available was also an issue. The solution chosen by JWST was to integrate the use of a Citrix environment with the DOORS database to address most of the project concerns. The use of the Citrix solution allowed a single Requirements database in a secure environment via a web interface. The Citrix environment allows JWST to upgrade to the most current version of DOORS without having to coordinate multiple sites and user upgrades. The single requirements database eliminates a multitude of Configuration Management concerns and facilitated the standardization of documentation formats. This paper discusses the obstacles and the lessons learned throughout the installation, implementation, usage and deployment process of a centralized DOORS database solution.

THE NASA AMES POLYCYCLIC AROMATIC HYDROCARBON INFRARED SPECTROSCOPIC DATABASE: THE COMPUTED SPECTRA

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

Bauschlicher, C. W.; Ricca, A.; Boersma, C.

The astronomical emission features, formerly known as the unidentified infrared bands, are now commonly ascribed to polycyclic aromatic hydrocarbons (PAHs). The laboratory experiments and computational modeling done at the NASA Ames Research Center to create a collection of PAH IR spectra relevant to test and refine the PAH hypothesis have been assembled into a spectroscopic database. This database now contains over 800 PAH spectra spanning 2-2000 {mu}m (5000-5 cm{sup -1}). These data are now available on the World Wide Web at www.astrochem.org/pahdb. This paper presents an overview of the computational spectra in the database and the tools developed to analyzemore » and interpret astronomical spectra using the database. A description of the online and offline user tools available on the Web site is also presented.« less

Correspondence: World Wide Web access to the British Universities Human Embryo Database

PubMed Central

AITON, JAMES F.; MCDONOUGH, ARIANA; MCLACHLAN, JOHN C.; SMART, STEVEN D.; WHITEN, SUSAN C.

1997-01-01

The British Universities Human Embryo Database has been created by merging information from the Walmsley Collection of Human Embryos at the School of Biological and Medical Sciences, University of St Andrews and from the Boyd Collection of Human Embryos at the Department of Anatomy, University of Cambridge. The database has been made available electronically on the Internet and World Wide Web browsers can be used to implement interactive access to the information stored in the British Universities Human Embryo Database. The database can, therefore, be accessed and searched from remote sites and specific embryos can be identified in terms of their location, age, developmental stage, plane of section, staining technique, and other parameters. It is intended to add information from other similar collections in the UK as it becomes available. PMID:9034891

DIMA 3.0: Domain Interaction Map.

PubMed

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

Double-u double-u double-u dot APIC dot org: a review of the APIC World Wide Web site.

PubMed

Harr, J

1996-12-01

The widespread use of the Internet and the development of the World Wide Web have led to a revolution in electronic communication and information access. The Association for Professional in Infection Control and Epidemiology (APIC) has developed a site on the World Wide Web to provide mechanisms for international on-line information access and exchange on issues related to the practice of infection control and the application of epidemiology. From the home page of the APIC Web site, users can access information on professional resources, publications, educational offering, governmental affairs, the APIC organization, and the infection control profession. Among the chief features of the site is a discussion forum for posing questions and sharing information about infection control and epidemiology. The site also contains a searchable database of practice-related abstracts and descriptions and order forms for APIC publications. Users will find continuing education course descriptions and registration forms, legislative and regulatory action alerts and a congressional mailer, chapter and committee information, and infection control information of interest to the general public. APIC is considering several potential future enhancements to their Web site and will continue to review the site's content and features to provide current and useful information to infection control professionals.

Intelligent web image retrieval system

NASA Astrophysics Data System (ADS)

Hong, Sungyong; Lee, Chungwoo; Nah, Yunmook

2001-07-01

Recently, the web sites such as e-business sites and shopping mall sites deal with lots of image information. To find a specific image from these image sources, we usually use web search engines or image database engines which rely on keyword only retrievals or color based retrievals with limited search capabilities. This paper presents an intelligent web image retrieval system. We propose the system architecture, the texture and color based image classification and indexing techniques, and representation schemes of user usage patterns. The query can be given by providing keywords, by selecting one or more sample texture patterns, by assigning color values within positional color blocks, or by combining some or all of these factors. The system keeps track of user's preferences by generating user query logs and automatically add more search information to subsequent user queries. To show the usefulness of the proposed system, some experimental results showing recall and precision are also explained.

Successful Keyword Searching: Initiating Research on Popular Topics Using Electronic Databases.

ERIC Educational Resources Information Center

MacDonald, Randall M.; MacDonald, Susan Priest

Students are using electronic resources more than ever before to locate information for assignments. Without the proper search terms, results are incomplete, and students are frustrated. Using the keywords, key people, organizations, and Web sites provided in this book and compiled from the most commonly used databases, students will be able to…

Non-Coding RNA Analysis Using the Rfam Database.

PubMed

Kalvari, Ioanna; Nawrocki, Eric P; Argasinska, Joanna; Quinones-Olvera, Natalia; Finn, Robert D; Bateman, Alex; Petrov, Anton I

2018-06-01

Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site. The data produced by Rfam have a broad application, from genome annotation to providing training sets for algorithm development. This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://rfam.org. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis

PubMed Central

Marsh, Terence L.; Saxman, Paul; Cole, James; Tiedje, James

2000-01-01

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms. PMID:10919828

40 CFR 63.567 - Recordkeeping and reporting requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the initial performance test and maintain in an accessible location on site an engineering report... this requirement to be submitted electronically into EPA's WebFIRE database. (2) All reports required...

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs. PMID:20624715

An overview of Airborne Data for Assessing Models (ADAM): a web development effort to effectively disseminate airborne data products

NASA Astrophysics Data System (ADS)

Mangosing, D. C.; Chen, G.; Kusterer, J.; Rinsland, P.; Perez, J.; Sorlie, S.; Parker, L.

2011-12-01

One of the objectives of the NASA Langley Research Center's MEaSURES project, "Creating a Unified Airborne Database for Model Assessment", is the development of airborne Earth System Data Records (ESDR) for the regional and global model assessment and validation activities performed by the tropospheric chemistry and climate modeling communities. The ongoing development of ADAM, a web site designed to access a unified, standardized and relational ESDR database, meets this objective. The ESDR database is derived from publically available data sets, from NASA airborne field studies to airborne and in-situ studies sponsored by NOAA, NSF, and numerous international partners. The ADAM web development activities provide an opportunity to highlight a growing synergy between the Airborne Science Data for Atmospheric Composition (ASD-AC) group at NASA Langley and the NASA Langley's Atmospheric Sciences Data Center (ASDC). These teams will collaborate on the ADAM web application by leveraging the state-of-the-art service and message-oriented data distribution architecture developed and implemented by ASDC and using a web-based tool provided by the ASD-AC group whose user interface accommodates the nuanced perspective of science users in the atmospheric chemistry and composition and climate modeling communities.

Applications of the U.S. Geological Survey's global land cover product

USGS Publications Warehouse

Reed, B.

1997-01-01

The U.S. Geological Survey (USGS), in partnership with several international agencies and universities, has produced a global land cover characteristics database. The land cover data were created using multitemporal analysis of advanced very high resolution radiometer satellite images in conjunction with other existing geographic data. A translation table permits the conversion of the land cover classes into several conventional land cover schemes that are used by ecosystem modelers, climate modelers, land management agencies, and other user groups. The alternative classification schemes include Global Ecosystems, the Biosphere Atmosphere Transfer Scheme, the Simple Biosphere, the USGS Anderson Level 2, and the International Geosphere Biosphere Programme. The distribution system for these data is through the World Wide Web (the web site address is: http://edcwww.cr.usgs.gov/landdaac/glcc/glcc.html) or by magnetic media upon special request The availability of the data over the World Wide Web, in conjunction with the flexible database structure, allows easy data access to a wide range of users. The web site contains a user registration form that allows analysis of the diverse applications of large-area land cover data. Currently, applications are divided among mapping (20 percent), conservation (30 percent), and modeling (35 percent).

48 CFR 252.204-7007 - Alternate A, Annual Representations and Certifications.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., Economic Price Adjustment-Wage Rates or Material Prices Controlled by a Foreign Government. Applies to... Certifications Application (ORCA) Web site at https://orca.bpn.gov/. After reviewing the ORCA database...

IMAGESEER - IMAGEs for Education and Research

NASA Technical Reports Server (NTRS)

Le Moigne, Jacqueline; Grubb, Thomas; Milner, Barbara

2012-01-01

IMAGESEER is a new Web portal that brings easy access to NASA image data for non-NASA researchers, educators, and students. The IMAGESEER Web site and database are specifically designed to be utilized by the university community, to enable teaching image processing (IP) techniques on NASA data, as well as to provide reference benchmark data to validate new IP algorithms. Along with the data and a Web user interface front-end, basic knowledge of the application domains, benchmark information, and specific NASA IP challenges (or case studies) are provided.

Database resources of the National Center for Biotechnology Information: 2002 update

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2002-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:11752242

Implementing a low-cost web-based clinical trial management system for community studies: a case study.

PubMed

Geyer, John; Myers, Kathleen; Vander Stoep, Ann; McCarty, Carolyn; Palmer, Nancy; DeSalvo, Amy

2011-10-01

Clinical trials with multiple intervention locations and a single research coordinating center can be logistically difficult to implement. Increasingly, web-based systems are used to provide clinical trial support with many commercial, open source, and proprietary systems in use. New web-based tools are available which can be customized without programming expertise to deliver web-based clinical trial management and data collection functions. To demonstrate the feasibility of utilizing low-cost configurable applications to create a customized web-based data collection and study management system for a five intervention site randomized clinical trial establishing the efficacy of providing evidence-based treatment via teleconferencing to children with attention-deficit hyperactivity disorder. The sites are small communities that would not usually be included in traditional randomized trials. A major goal was to develop database that participants could access from computers in their home communities for direct data entry. Discussed is the selection process leading to the identification and utilization of a cost-effective and user-friendly set of tools capable of customization for data collection and study management tasks. An online assessment collection application, template-based web portal creation application, and web-accessible Access 2007 database were selected and customized to provide the following features: schedule appointments, administer and monitor online secure assessments, issue subject incentives, and securely transmit electronic documents between sites. Each tool was configured by users with limited programming expertise. As of June 2011, the system has successfully been used with 125 participants in 5 communities, who have completed 536 sets of assessment questionnaires, 8 community therapists, and 11 research staff at the research coordinating center. Total automation of processes is not possible with the current set of tools as each is loosely affiliated, creating some inefficiency. This system is best suited to investigations with a single data source e.g., psychosocial questionnaires. New web-based applications can be used by investigators with limited programming experience to implement user-friendly, efficient, and cost-effective tools for multi-site clinical trials with small distant communities. Such systems allow the inclusion in research of populations that are not usually involved in clinical trials.

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

Geothopica and the interactive analysis and visualization of the updated Italian National Geothermal Database

NASA Astrophysics Data System (ADS)

Trumpy, Eugenio; Manzella, Adele

2017-02-01

The Italian National Geothermal Database (BDNG), is the largest collection of Italian Geothermal data and was set up in the 1980s. It has since been updated both in terms of content and management tools: information on deep wells and thermal springs (with temperature > 30 °C) are currently organized and stored in a PostgreSQL relational database management system, which guarantees high performance, data security and easy access through different client applications. The BDNG is the core of the Geothopica web site, whose webGIS tool allows different types of user to access geothermal data, to visualize multiple types of datasets, and to perform integrated analyses. The webGIS tool has been recently improved by two specially designed, programmed and implemented visualization tools to display data on well lithology and underground temperatures. This paper describes the contents of the database and its software and data update, as well as the webGIS tool including the new tools for data lithology and temperature visualization. The geoinformation organized in the database and accessible through Geothopica is of use not only for geothermal purposes, but also for any kind of georesource and CO2 storage project requiring the organization of, and access to, deep underground data. Geothopica also supports project developers, researchers, and decision makers in the assessment, management and sustainable deployment of georesources.

The STP (Solar-Terrestrial Physics) Semantic Web based on the RSS1.0 and the RDF

NASA Astrophysics Data System (ADS)

Kubo, T.; Murata, K. T.; Kimura, E.; Ishikura, S.; Shinohara, I.; Kasaba, Y.; Watari, S.; Matsuoka, D.

2006-12-01

In the Solar-Terrestrial Physics (STP), it is pointed out that circulation and utilization of observation data among researchers are insufficient. To archive interdisciplinary researches, we need to overcome this circulation and utilization problems. Under such a background, authors' group has developed a world-wide database that manages meta-data of satellite and ground-based observation data files. It is noted that retrieving meta-data from the observation data and registering them to database have been carried out by hand so far. Our goal is to establish the STP Semantic Web. The Semantic Web provides a common framework that allows a variety of data shared and reused across applications, enterprises, and communities. We also expect that the secondary information related with observations, such as event information and associated news, are also shared over the networks. The most fundamental issue on the establishment is who generates, manages and provides meta-data in the Semantic Web. We developed an automatic meta-data collection system for the observation data using the RSS (RDF Site Summary) 1.0. The RSS1.0 is one of the XML-based markup languages based on the RDF (Resource Description Framework), which is designed for syndicating news and contents of news-like sites. The RSS1.0 is used to describe the STP meta-data, such as data file name, file server address and observation date. To describe the meta-data of the STP beyond RSS1.0 vocabulary, we defined original vocabularies for the STP resources using the RDF Schema. The RDF describes technical terms on the STP along with the Dublin Core Metadata Element Set, which is standard for cross-domain information resource descriptions. Researchers' information on the STP by FOAF, which is known as an RDF/XML vocabulary, creates a machine-readable metadata describing people. Using the RSS1.0 as a meta-data distribution method, the workflow from retrieving meta-data to registering them into the database is automated. This technique is applied for several database systems, such as the DARTS database system and NICT Space Weather Report Service. The DARTS is a science database managed by ISAS/JAXA in Japan. We succeeded in generating and collecting the meta-data automatically for the CDF (Common data Format) data, such as Reimei satellite data, provided by the DARTS. We also create an RDF service for space weather report and real-time global MHD simulation 3D data provided by the NICT. Our Semantic Web system works as follows: The RSS1.0 documents generated on the data sites (ISAS and NICT) are automatically collected by a meta-data collection agent. The RDF documents are registered and the agent extracts meta-data to store them in the Sesame, which is an open source RDF database with support for RDF Schema inferencing and querying. The RDF database provides advanced retrieval processing that has considered property and relation. Finally, the STP Semantic Web provides automatic processing or high level search for the data which are not only for observation data but for space weather news, physical events, technical terms and researches information related to the STP.

Thomson Scientific's expanding Web of Knowledge: beyond citation databases and current awareness services.

PubMed

London, Sue; Brahmi, Frances A

2005-01-01

As end-user demand for easy access to electronic full text continues to climb, an increasing number of information providers are combining that access with their other products and services, making navigating their Web sites by librarians seeking information on a given product or service more daunting than ever. One such provider of a complex array of products and services is Thomson Scientific. This paper looks at some of the many products and tools available from two of Thomson Scientific's businesses, Thomson ISI and Thomson ResearchSoft. Among the items of most interest to health sciences and veterinary librarians and their users are the variety of databases available via the ISI Web of Knowledge platform and the information management products available from ResearchSoft.

Web-based flood database for Colorado, water years 1867 through 2011

USGS Publications Warehouse

Kohn, Michael S.; Jarrett, Robert D.; Krammes, Gary S.; Mommandi, Amanullah

2013-01-01

In order to provide a centralized repository of flood information for the State of Colorado, the U.S. Geological Survey, in cooperation with the Colorado Department of Transportation, created a Web-based geodatabase for flood information from water years 1867 through 2011 and data for paleofloods occurring in the past 5,000 to 10,000 years. The geodatabase was created using the Environmental Systems Research Institute ArcGIS JavaScript Application Programing Interface 3.2. The database can be accessed at http://cwscpublic2.cr.usgs.gov/projects/coflood/COFloodMap.html. Data on 6,767 flood events at 1,597 individual sites throughout Colorado were compiled to generate the flood database. The data sources of flood information are indirect discharge measurements that were stored in U.S. Geological Survey offices (water years 1867–2011), flood data from indirect discharge measurements referenced in U.S. Geological Survey reports (water years 1884–2011), paleoflood studies from six peer-reviewed journal articles (data on events occurring in the past 5,000 to 10,000 years), and the U.S. Geological Survey National Water Information System peak-discharge database (water years 1883–2010). A number of tests were performed on the flood database to ensure the quality of the data. The Web interface was programmed using the Environmental Systems Research Institute ArcGIS JavaScript Application Programing Interface 3.2, which allows for display, query, georeference, and export of the data in the flood database. The data fields in the flood database used to search and filter the database include hydrologic unit code, U.S. Geological Survey station number, site name, county, drainage area, elevation, data source, date of flood, peak discharge, and field method used to determine discharge. Additional data fields can be viewed and exported, but the data fields described above are the only ones that can be used for queries.

75 FR 46943 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

...-capturing process. SAMHSA will place Web site registration information into a Knowledge Management database... September 3, 2010 to: SAMHSA Desk Officer, Human Resources and Housing Branch, Office of Management and...

PDB-Metrics: a web tool for exploring the PDB contents.

PubMed

Fileto, Renato; Kuser, Paula R; Yamagishi, Michel E B; Ribeiro, André A; Quinalia, Thiago G; Franco, Eduardo H; Mancini, Adauto L; Higa, Roberto H; Oliveira, Stanley R M; Santos, Edgard H; Vieira, Fabio D; Mazoni, Ivan; Cruz, Sergio A B; Neshich, Goran

2006-06-30

PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system.

A new information architecture, website and services for the CMS experiment

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

Taylor, Lucas; Rusack, Eleanor; Zemleris, Vidmantas

2012-01-01

The age and size of the CMS collaboration at the LHC means it now has many hundreds of inhomogeneous web sites and services, and hundreds of thousands of documents. We describe a major initiative to create a single coherent CMS internal and public web site. This uses the Drupal web Content Management System (now supported by CERN/IT) on top of a standard LAMP stack (Linux, Apache, MySQL, and php/perl). The new navigation, content and search services are coherently integrated with numerous existing CERN services (CDS, EDMS, Indico, phonebook, Twiki) as well as many CMS internal Web services. We describe themore » information architecture, the system design, implementation and monitoring, the document and content database, security aspects, and our deployment strategy, which ensured continual smooth operation of all systems at all times.« less

A new Information Architecture, Website and Services for the CMS Experiment

NASA Astrophysics Data System (ADS)

Taylor, Lucas; Rusack, Eleanor; Zemleris, Vidmantas

2012-12-01

The age and size of the CMS collaboration at the LHC means it now has many hundreds of inhomogeneous web sites and services, and hundreds of thousands of documents. We describe a major initiative to create a single coherent CMS internal and public web site. This uses the Drupal web Content Management System (now supported by CERN/IT) on top of a standard LAMP stack (Linux, Apache, MySQL, and php/perl). The new navigation, content and search services are coherently integrated with numerous existing CERN services (CDS, EDMS, Indico, phonebook, Twiki) as well as many CMS internal Web services. We describe the information architecture; the system design, implementation and monitoring; the document and content database; security aspects; and our deployment strategy, which ensured continual smooth operation of all systems at all times.

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

Jung, Haeryong; Lee, Eunyong; Jeong, YiYeong

Korea Radioactive-waste Management Corporation (KRMC) established in 2009 has started a new project to collect information on long-term stability of deep geological environments on the Korean Peninsula. The information has been built up in the integrated natural barrier database system available on web (www.deepgeodisposal.kr). The database system also includes socially and economically important information, such as land use, mining area, natural conservation area, population density, and industrial complex, because some of this information is used as exclusionary criteria during the site selection process for a deep geological repository for safe and secure containment and isolation of spent nuclear fuel andmore » other long-lived radioactive waste in Korea. Although the official site selection process has not been started yet in Korea, current integrated natural barrier database system and socio-economic database is believed that the database system will be effectively utilized to narrow down the number of sites where future investigation is most promising in the site selection process for a deep geological repository and to enhance public acceptance by providing readily-available relevant scientific information on deep geological environments in Korea. (authors)« less

MyEnviroMapper

EPA Pesticide Factsheets

EnviroMapper for Envirofacts is a single point of access to select U.S. EPA environmental data. This Web site provides access to several EPA databases to provide you with information about environmental activities that may affect air, water, and l

Ocean Instruments Web Site for Undergraduate, Secondary and Informal Education

NASA Astrophysics Data System (ADS)

Farrington, J. W.; Nevala, A.; Dolby, L. A.

2004-12-01

An Ocean Instruments web site has been developed that makes available information about ocean sampling and measurement instruments and platforms. The site features text, pictures, diagrams and background information written or edited by experts in ocean science and engineering and contains links to glossaries and multimedia technologies including video streaming, audio packages, and searchable databases. The site was developed after advisory meetings with selected professors teaching undergraduate classes who responded to the question, what could Woods Hole Oceanographic Institution supply to enhance undergraduate education in ocean sciences, life sciences, and geosciences? Prototypes were developed and tested with students, potential users, and potential contributors. The site is hosted by WHOI. The initial five instruments featured were provided by four WHOI scientists and engineers and by one Sea Education Association faculty member. The site is now open to contributions from scientists and engineers worldwide. The site will not advertise or promote the use of individual ocean instruments.

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

PubMed Central

You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Luan, Yijie; Tian, Peng; Chen, Liangfu; Huang, Guangrui; Huang, Shengfeng; Li, Yuxin; Li, Jie; Chen, Chengyong; Zhang, Yaqing; Chen, Shangwu; Xu, Anlong

2015-01-01

Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish. PMID:25378337

Interface Between CDS/ISIS and the Web at the Library of the Cagliari Observatory

NASA Astrophysics Data System (ADS)

Mureddu, Leonardo; Denotti, Franca; Alvito, Gianni

The library catalog of the Cagliari Observatory was digitized some years ago, by using CDS/ISIS with a practical format named ``ASTCA'' derived from the well-known ``BIBLO''. Recently the observatory has put some effort into the creation and maintenance of a Web site; on that occasion the library database has been interfaced to the Web server by means of the software WWWISIS and a locally created search form. Both books and journals can be searched by remote users. Book searches can be made by authors, titles or keywords.

Patient-oriented cancer information on the internet: a comparison of wikipedia and a professionally maintained database.

PubMed

Rajagopalan, Malolan S; Khanna, Vineet K; Leiter, Yaacov; Stott, Meghan; Showalter, Timothy N; Dicker, Adam P; Lawrence, Yaacov R

2011-09-01

A wiki is a collaborative Web site, such as Wikipedia, that can be freely edited. Because of a wiki's lack of formal editorial control, we hypothesized that the content would be less complete and accurate than that of a professional peer-reviewed Web site. In this study, the coverage, accuracy, and readability of cancer information on Wikipedia were compared with those of the patient-orientated National Cancer Institute's Physician Data Query (PDQ) comprehensive cancer database. For each of 10 cancer types, medically trained personnel scored PDQ and Wikipedia articles for accuracy and presentation of controversies by using an appraisal form. Reliability was assessed by using interobserver variability and test-retest reproducibility. Readability was calculated from word and sentence length. Evaluators were able to rapidly assess articles (18 minutes/article), with a test-retest reliability of 0.71 and interobserver variability of 0.53. For both Web sites, inaccuracies were rare, less than 2% of information examined. PDQ was significantly more readable than Wikipedia: Flesch-Kincaid grade level 9.6 versus 14.1. There was no difference in depth of coverage between PDQ and Wikipedia (29.9, 34.2, respectively; maximum possible score 72). Controversial aspects of cancer care were relatively poorly discussed in both resources (2.9 and 6.1 for PDQ and Wikipedia, respectively, NS; maximum possible score 18). A planned subanalysis comparing common and uncommon cancers demonstrated no difference. Although the wiki resource had similar accuracy and depth as the professionally edited database, it was significantly less readable. Further research is required to assess how this influences patients' understanding and retention.

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana.

PubMed

Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

2016-10-18

N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. The server also provides a comprehensive database of predicted transcriptome-wide m 6 A sites and curated m 6 A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at .

Construction of web-based nutrition education contents and searching engine for usage of healthy menu of children

PubMed Central

Lee, Tae-Kyong; Chung, Hea-Jung; Park, Hye-Kyung; Lee, Eun-Ju; Nam, Hye-Seon; Jung, Soon-Im; Cho, Jee-Ye; Lee, Jin-Hee; Kim, Gon; Kim, Min-Chan

2008-01-01

A diet habit, which is developed in childhood, lasts for a life time. In this sense, nutrition education and early exposure to healthy menus in childhood is important. Children these days have easy access to the internet. Thus, a web-based nutrition education program for children is an effective tool for nutrition education of children. This site provides the material of the nutrition education for children with characters which are personified nutrients. The 151 menus are stored in the site together with video script of the cooking process. The menus are classified by the criteria based on age, menu type and the ethnic origin of the menu. The site provides a search function. There are three kinds of search conditions which are key words, menu type and "between" expression of nutrients such as calorie and other nutrients. The site is developed with the operating system Windows 2003 Server, the web server ZEUS 5, development language JSP, and database management system Oracle 10 g. PMID:20126375

Development of a geotechnical information database.

DOT National Transportation Integrated Search

2009-08-01

The purpose of this project was to create a user-friendly geotechnical Web site, so the LADOTD Headquarters Geotechnical Design Section and other LADOTD sections will have access to the appropriate and necessary resources to make the best design d...

Error Tracking System

EPA Pesticide Factsheets

Error Tracking System is a database used to store & track error notifications sent by users of EPA's web site. ETS is managed by OIC/OEI. OECA's ECHO & OEI Envirofacts use it. Error notifications from EPA's home Page under Contact Us also uses it.

MaGa, a web-based collaborative database for gas emissions: a tool to improve the knowledge on Earth degassing

NASA Astrophysics Data System (ADS)

Frigeri, A.; Cardellini, C.; Chiodini, G.; Frondini, F.; Bagnato, E.; Aiuppa, A.; Fischer, T. P.; Lehnert, K. A.

2014-12-01

The study of the main pathways of carbon flux from the deep Earth requires the analysis of a large quantity and variety of data on volcanic and non-volcanic gas emissions. Hence, there is need for common frameworks to aggregate available data and insert new observations. Since 2010 we have been developing the Mapping Gas emissions (MaGa) web-based database to collect data on carbon degassing form volcanic and non-volcanic environments. MaGa uses an Object-relational model, translating the experience of field surveyors into the database schema. The current web interface of MaGa allows users to browse the data in tabular format or by browsing an interactive web-map. Enabled users can insert information as measurement methods, instrument details as well as the actual values collected in the field. Measurements found in the literature can be inserted as well as direct field observations made by human-operated instruments. Currently the database includes fluxes and gas compositions from active craters degassing, diffuse soil degassing and fumaroles both from dormant volcanoes and open-vent volcanoes from literature survey and data about non-volcanic emission of the Italian territory. Currently, MaGa holds more than 1000 volcanic plume degassing fluxes, data from 30 sites of diffuse soil degassing from italian volcanoes, and about 60 measurements from fumarolic and non volcanic emission sites. For each gas emission site, the MaGa holds data, pictures, descriptions on gas sampling, analysis and measurement methods, together with bibliographic references and contacts to researchers having experience on each site. From 2012, MaGa developments started to be focused towards the framework of the Deep Earth Carbon Degassing research initiative of the Deep Carbon Observatory. Whithin the DECADE initiative, there are others data systems, as EarthChem and the Smithsonian Institution's Global Volcanism Program. An interoperable interaction between the DECADE data systems is being planned. MaGa is showing good potentials to improve the knowledge on Earth degassing firstly by making data more accessible and encouraging participation among researchers, and secondly by allowing to observe and explore, for the first time, a gas emission dataset with spatial and temporal extents never analyzed before.

Insights on WWW-based geoscience teaching: Climbing the first year learning cliff

NASA Astrophysics Data System (ADS)

Lamberson, Michelle N.; Johnson, Mark; Bevier, Mary Lou; Russell, J. Kelly

1997-06-01

In early 1995, The University of British Columbia Department of Geological Sciences (now Earth and Ocean Sciences) initiated a project that explored the effectiveness of the World Wide Web as a teaching and learning medium. Four decisions made at the onset of the project have guided the department's educational technology plan: (1) over 90% of funding recieved from educational technology grants was committed towards personnel; (2) materials developed are modular in design; (3) a data-base approach was taken to resource development; and (4) a strong commitment to student involvement in courseware development. The project comprised development of a web site for an existing core course: Geology 202, Introduction to Petrology. The web site is a gateway to course information, content, resources, exercises, and several searchable data-bases (images, petrologic definitions, and minerals in thin section). Material was developed on either an IBM or UNIX machine, ported to a UNIX platform, and is accessed using the Netscape browser. The resources consist primarily of HTML files or CGI scripts with associated text, images, sound, digital movies, and animations. Students access the web site from the departmental student computer facility, from home or a computer station in the petrology laboratory. Results of a survey of the Geol 202 students indicate that they found the majority of the resources useful, and the site is being expanded. The Geology 202 project had a "trickle-up" effect throughout the department: prior to this project, there was minimal use of Internet resources in lower-level geology courses. By the end of the 1996-1997 academic year, we anticipate that at least 17 Earth and Ocean Science courses will have a WWW site for one or all of the following uses: (1) presenting basic information; (2) accessing lecture images; (3) providing a jumping-off point for exploring related WWW sites; (4) conducting on-line exercises; and/or (5) providing a communications forum for students and faculty via a Hypernews group. Url http://www.science.ubc.ca/

Academic medical center libraries on the Web.

PubMed Central

Tannery, N H; Wessel, C B

1998-01-01

Academic medical center libraries are moving towards publishing electronically, utilizing networked technologies, and creating digital libraries. The catalyst for this movement has been the Web. An analysis of academic medical center library Web pages was undertaken to assess the information created and communicated in early 1997. A summary of present uses and suggestions for future applications is provided. A method for evaluating and describing the content of library Web sites was designed. The evaluation included categorizing basic information such as description and access to library services, access to commercial databases, and use of interactive forms. The main goal of the evaluation was to assess original resources produced by these libraries. PMID:9803298

The Tropical Biominer Project: mining old sources for new drugs.

PubMed

Artiguenave, François; Lins, André; Maciel, Wesley Dias; Junior, Antonio Celso Caldeira; Nacif-Coelho, Carla; de Souza Linhares, Maria Margarida Ribeiro; de Oliveira, Guilherme Correa; Barbosa, Luis Humberto Rezende; Lopes, Júlio César Dias; Junior, Claudionor Nunes Coelho

2005-01-01

The Tropical Biominer Project is a recent initiative from the Federal University of Minas Gerais (UFMG) and the Oswaldo Cruz foundation, with the participation of the Biominas Foundation (Belo Horizonte, Minas Gerais, Brazil) and the start-up Homologix. The main objective of the project is to build a new resource for the chemogenomics research, on chemical compounds, with a strong emphasis on natural molecules. Adopted technologies include the search of information from structured, semi-structured, and non-structured documents (the last two from the web) and datamining tools in order to gather information from different sources. The database is the support for developing applications to find new potential treatments for parasitic infections by using virtual screening tools. We present here the midpoint of the project: the conception and implementation of the Tropical Biominer Database. This is a Federated Database designed to store data from different resources. Connected to the database, a web crawler is able to gather information from distinct, patented web sites and store them after automatic classification using datamining tools. Finally, we demonstrate the interest of the approach, by formulating new hypotheses on specific targets of a natural compound, violacein, using inferences from a Virtual Screening procedure.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Kenton, David L.; Khovayko, Oleg; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Sherry, Stephen T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Suzek, Tugba O.; Tatusov, Roman; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2006-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840

Database resources of the National Center for Biotechnology Information

PubMed Central

Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

2014-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2001-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:11125038

Database resources of the National Center for Biotechnology

PubMed Central

Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

2003-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941

SoyFN: a knowledge database of soybean functional networks.

PubMed

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

Web-based Visualization and Query of semantically segmented multiresolution 3D Models in the Field of Cultural Heritage

NASA Astrophysics Data System (ADS)

Auer, M.; Agugiaro, G.; Billen, N.; Loos, L.; Zipf, A.

2014-05-01

Many important Cultural Heritage sites have been studied over long periods of time by different means of technical equipment, methods and intentions by different researchers. This has led to huge amounts of heterogeneous "traditional" datasets and formats. The rising popularity of 3D models in the field of Cultural Heritage in recent years has brought additional data formats and makes it even more necessary to find solutions to manage, publish and study these data in an integrated way. The MayaArch3D project aims to realize such an integrative approach by establishing a web-based research platform bringing spatial and non-spatial databases together and providing visualization and analysis tools. Especially the 3D components of the platform use hierarchical segmentation concepts to structure the data and to perform queries on semantic entities. This paper presents a database schema to organize not only segmented models but also different Levels-of-Details and other representations of the same entity. It is further implemented in a spatial database which allows the storing of georeferenced 3D data. This enables organization and queries by semantic, geometric and spatial properties. As service for the delivery of the segmented models a standardization candidate of the OpenGeospatialConsortium (OGC), the Web3DService (W3DS) has been extended to cope with the new database schema and deliver a web friendly format for WebGL rendering. Finally a generic user interface is presented which uses the segments as navigation metaphor to browse and query the semantic segmentation levels and retrieve information from an external database of the German Archaeological Institute (DAI).

A Geospatial Database that Supports Derivation of Climatological Features of Severe Weather

NASA Astrophysics Data System (ADS)

Phillips, M.; Ansari, S.; Del Greco, S.

2007-12-01

The Severe Weather Data Inventory (SWDI) at NOAA's National Climatic Data Center (NCDC) provides user access to archives of several datasets critical to the detection and evaluation of severe weather. These datasets include archives of: · NEXRAD Level-III point features describing general storm structure, hail, mesocyclone and tornado signatures · National Weather Service Storm Events Database · National Weather Service Local Storm Reports collected from storm spotters · National Weather Service Warnings · Lightning strikes from Vaisala's National Lightning Detection Network (NLDN) SWDI archives all of these datasets in a spatial database that allows for convenient searching and subsetting. These data are accessible via the NCDC web site, Web Feature Services (WFS) or automated web services. The results of interactive web page queries may be saved in a variety of formats, including plain text, XML, Google Earth's KMZ, standards-based NetCDF and Shapefile. NCDC's Storm Risk Assessment Project (SRAP) uses data from the SWDI database to derive gridded climatology products that show the spatial distributions of the frequency of various events. SRAP also can relate SWDI events to other spatial data such as roads, population, watersheds, and other geographic, sociological, or economic data to derive products that are useful in municipal planning, emergency management, the insurance industry, and other areas where there is a need to quantify and qualify how severe weather patterns affect people and property.

HippDB: a database of readily targeted helical protein-protein interactions.

PubMed

Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

2013-11-01

HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

TreeVector: scalable, interactive, phylogenetic trees for the web.

PubMed

Pethica, Ralph; Barker, Gary; Kovacs, Tim; Gough, Julian

2010-01-28

Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees. We introduce TreeVector, a Scalable Vector Graphics-and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print. TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user's own web server. It has already been deployed on two recognized and widely used database Web sites.

U.S. Quaternary Fault and Fold Database Released

NASA Astrophysics Data System (ADS)

Haller, Kathleen M.; Machette, Michael N.; Dart, Richard L.; Rhea, B. Susan

2004-06-01

A comprehensive online compilation of Quaternary-age faults and folds throughout the United States was recently released by the U.S. Geological Survey, with cooperation from state geological surveys, academia, and the private sector. The Web site at http://Qfaults.cr.usgs.gov/ contains searchable databases and related geo-spatial data that characterize earthquake-related structures that could be potential seismic sources for large-magnitude (M > 6) earthquakes.

The Ensembl Web Site: Mechanics of a Genome Browser

PubMed Central

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V.

2004-01-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species. PMID:15123591

The Ensembl Web site: mechanics of a genome browser.

PubMed

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V

2004-05-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

Introduction of the American Academy of Facial Plastic and Reconstructive Surgery FACE TO FACE Database.

PubMed

Abraham, Manoj T; Rousso, Joseph J; Hu, Shirley; Brown, Ryan F; Moscatello, Augustine L; Finn, J Charles; Patel, Neha A; Kadakia, Sameep P; Wood-Smith, Donald

2017-07-01

The American Academy of Facial Plastic and Reconstructive Surgery FACE TO FACE database was created to gather and organize patient data primarily from international humanitarian surgical mission trips, as well as local humanitarian initiatives. Similar to cloud-based Electronic Medical Records, this web-based user-generated database allows for more accurate tracking of provider and patient information and outcomes, regardless of site, and is useful when coordinating follow-up care for patients. The database is particularly useful on international mission trips as there are often different surgeons who may provide care to patients on subsequent missions, and patients who may visit more than 1 mission site. Ultimately, by pooling data across multiples sites and over time, the database has the potential to be a useful resource for population-based studies and outcome data analysis. The objective of this paper is to delineate the process involved in creating the AAFPRS FACE TO FACE database, to assess its functional utility, to draw comparisons to electronic medical records systems that are now widely implemented, and to explain the specific benefits and disadvantages of the use of the database as it was implemented on recent international surgical mission trips.

BioData: a national aquatic bioassessment database

USGS Publications Warehouse

MacCoy, Dorene

2011-01-01

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services. BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 816 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 477 samples from 39 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis. BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN's). A simple web-data input interface and self-guided, public data-retrieval web site provides access to bioassessment data. BioData currently accepts data collected using two national protocols: (1) NAWQA and (2) U.S. Environmental Protection Agency (USEPA) National Rivers and Streams Assessment (NRSA). Additional collection protocols are planned for future versions.

From Chaos to Content: An Integrated Approach to Government Web Sites

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

Demuth, Nora H.; Knudson, Christa K.

2005-01-03

The web development team of the Environmental Technology Directorate (ETD) at the U.S. Department of Energy’s Pacific Northwest National Laboratory (PNNL) redesigned the ETD website as a database-driven system, powered by the newly designed ETD Common Information System (ETD-CIS). The ETD website was redesigned in response to an analysis that showed the previous ETD websites were inefficient, costly, and lacking in a consistent focus. Redesigned and newly created websites based on a new ETD template provide a consistent image, meet or exceed accessibility standards, and are linked through a common database. The protocols used in developing the ETD website supportmore » integration of further organizational sites and facilitate internal use by staff and training on ETD website development and maintenance. Other PNNL organizations have approached the ETD web development team with an interest in applying the methods established by the ETD system. The ETD system protocol could potentially be used by other DOE laboratories to improve their website efficiency and content focus. “The tools by which we share science information must be as extraordinary as the information itself.[ ]” – DOE Science Director Raymond Orbach« less

eSciMart: Web Platform for Scientific Software Marketplace

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-10-01

In this paper we suggest a design of a web marketplace where users of scientific application software and databases, presented in the form of web services, as well as their providers will have presence simultaneously. The model, which will be the basis for the web marketplace is close to the customer-to-customer (C2C) model, which has been successfully used, for example, on the auction sites such as eBay (ebay.com). Unlike the classical model of C2C the suggested marketplace focuses on application software in the form of web services, and standardization of API through which application software will be integrated into the web marketplace. A prototype of such a platform, entitled eSciMart, is currently being developed at SINP MSU.

NGL Viewer: a web application for molecular visualization

PubMed Central

Rose, Alexander S.; Hildebrand, Peter W.

2015-01-01

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. ‘cartoon, spacefill, licorice’). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations. PMID:25925569

Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

PubMed Central

Keator, David B.; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R.; Bockholt, Jeremy; Grethe, Jeffrey S.

2010-01-01

Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site. PMID:20567938

Federated web-accessible clinical data management within an extensible neuroimaging database.

PubMed

Ozyurt, I Burak; Keator, David B; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R; Bockholt, Jeremy; Grethe, Jeffrey S

2010-12-01

Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site.

COMET Multimedia modules and objects in the digital library system

NASA Astrophysics Data System (ADS)

Spangler, T. C.; Lamos, J. P.

2003-12-01

Over the past ten years of developing Web- and CD-ROM-based training materials, the Cooperative Program for Operational Meteorology, Education and Training (COMET) has created a unique archive of almost 10,000 multimedia objects and some 50 web based interactive multimedia modules on various aspects of weather and weather forecasting. These objects and modules, containing illustrations, photographs, animations,video sequences, audio files, are potentially a valuable resource for university faculty and students, forecasters, emergency managers, public school educators, and other individuals and groups needing such materials for educational use. The COMET Modules are available on the COMET educational web site http://www.meted.ucar.edu, and the COMET Multimedia Database (MMDB) makes a collection of the multimedia objects available in a searchable online database for viewing and download over the Internet. Some 3200 objects are already available at the MMDB Website: http://archive.comet.ucar.edu/moria/

Textpresso site-specific recombinases: A text-mining server for the recombinase literature including Cre mice and conditional alleles.

PubMed

Urbanski, William M; Condie, Brian G

2009-12-01

Textpresso Site Specific Recombinases (http://ssrc.genetics.uga.edu/) is a text-mining web server for searching a database of more than 9,000 full-text publications. The papers and abstracts in this database represent a wide range of topics related to site-specific recombinase (SSR) research tools. Included in the database are most of the papers that report the characterization or use of mouse strains that express Cre recombinase as well as papers that describe or analyze mouse lines that carry conditional (floxed) alleles or SSR-activated transgenes/knockins. The database also includes reports describing SSR-based cloning methods such as the Gateway or the Creator systems, papers reporting the development or use of SSR-based tools in systems such as Drosophila, bacteria, parasites, stem cells, yeast, plants, zebrafish, and Xenopus as well as publications that describe the biochemistry, genetics, or molecular structure of the SSRs themselves. Textpresso Site Specific Recombinases is the only comprehensive text-mining resource available for the literature describing the biology and technical applications of SSRs. (c) 2009 Wiley-Liss, Inc.

The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

PubMed

Chen, Yi-Bu; Chattopadhyay, Ansuman; Bergen, Phillip; Gadd, Cynthia; Tannery, Nancy

2007-01-01

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc).

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

NASA Technical Reports Server (NTRS)

Moore, Reagan; Marciano, Richard; Wan, Michael; Sherwin, Tom; Frost, Richard

1996-01-01

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

Drug-Path: a database for drug-induced pathways

PubMed Central

Zeng, Hui; Cui, Qinghua

2015-01-01

Some databases for drug-associated pathways have been built and are publicly available. However, the pathways curated in most of these databases are drug-action or drug-metabolism pathways. In recent years, high-throughput technologies such as microarray and RNA-sequencing have produced lots of drug-induced gene expression profiles. Interestingly, drug-induced gene expression profile frequently show distinct patterns, indicating that drugs normally induce the activation or repression of distinct pathways. Therefore, these pathways contribute to study the mechanisms of drugs and drug-repurposing. Here, we present Drug-Path, a database of drug-induced pathways, which was generated by KEGG pathway enrichment analysis for drug-induced upregulated genes and downregulated genes based on drug-induced gene expression datasets in Connectivity Map. Drug-Path provides user-friendly interfaces to retrieve, visualize and download the drug-induced pathway data in the database. In addition, the genes deregulated by a given drug are highlighted in the pathways. All data were organized using SQLite. The web site was implemented using Django, a Python web framework. Finally, we believe that this database will be useful for related researches. Database URL: http://www.cuilab.cn/drugpath PMID:26130661

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

The Internet as a communication tool for orthopedic spine fellowships in the United States.

PubMed

Silvestre, Jason; Guzman, Javier Z; Skovrlj, Branko; Overley, Samuel C; Cho, Samuel K; Qureshi, Sheeraz A; Hecht, Andrew C

2015-04-01

Orthopedic residents seeking additional training in spine surgery commonly use the Internet to manage their fellowship applications. Although studies have assessed the accessibility and content of Web sites in other medical specialties, none have looked at orthopedic spine fellowship Web sites (SFWs). The purpose of this study was to evaluate the accessibility of information from commonly used databases and assess the content of SFWs. This was a Web site accessibility and content evaluation study. A comprehensive list of available orthopedic spine fellowship programs was compiled by accessing program lists from the SF Match, North American Spine Society, Fellowship and Residency Electronic Interactive Database (FREIDA), and Orthopaedicsone.com (Ortho1). These databases were assessed for accessibility of information including viable links to SFWs and responsive program contacts. A Google search was used to identify SFWs not readily available on these national databases. SFWs were evaluated based on online education and recruitment content. Evaluators found 45 SFWs of 63 active programs (71%). Available SFWs were often not readily accessible from national program lists, and no program afforded a direct link to their SFW from SF Match. Approximately half of all programs responded via e-mail. Although many programs described surgical experience (91%) and research requirements (87%) during the fellowship, less than half mentioned didactic instruction (46%), journal clubs (41%), and national meetings or courses attended (28%). Evaluators found an average 45% of fellow recruitment content. Comparison of SFWs by program characteristics revealed three significant differences. Programs with greater than one fellowship position had greater online education content than programs with a single fellow (p=.022). Spine fellowships affiliated with an orthopedic residency program maintained greater education (p=.006) and recruitment (p=.046) content on their SFWs. Most orthopedic spine surgery programs underuse the Internet for fellow education and recruitment. The inaccessibility of information and paucity of content on SFWs allow for future opportunity to optimize these resources. Copyright © 2015 Elsevier Inc. All rights reserved.

79 FR 77522 - Public Review of the Draft Part 2 (Revision), Digital Orthoimagery, of the Federal Geographic...

Federal Register 2010, 2011, 2012, 2013, 2014

2014-12-24

... for the semantic content of orthoimagery databases for public agencies and private enterprises. It... to the public on the FGDC Web site, www.fgdc.gov . DATES: Comments on the draft Part 2 (revision...

Free Web resources on alternatives.

PubMed

Donnelly, Thomas M

2004-03-01

Access to many online databases for alternatives searches requires a paid subscription and these fees may be expensive for small or not-for-profit institutions. The author provides a list of free sites that can be used to fulfill the legal requirement for an alternatives search.

ESTuber db: an online database for Tuber borchii EST sequences.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cosentino, Cristian; Stella, Alessandra; Milanesi, Luciano; Viotti, Angelo

2007-03-08

The ESTuber database (http://www.itb.cnr.it/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface. Sequences included in the ESTuber db were clustered and annotated against three databases: the GenBank nr database, the UniProtKB database and a third in-house prepared database of fungi genomic sequences. An algorithm was implemented to infer statistical classification among Gene Ontology categories from the ontology occurrences deduced from the annotation procedure against the UniProtKB database. Ontologies were also deduced from the annotation of more than 130,000 EST sequences from five filamentous fungi, for intra-species comparison purposes. Further analyses were performed on the ESTuber db dataset, including tandem repeats search and comparison of the putative protein dataset inferred from the EST sequences to the PROSITE database for protein patterns identification. All the analyses were performed both on the complete sequence dataset and on the contig consensus sequences generated by the EST assembly procedure. The resulting web site is a resource of data and links related to truffle expressed genes. The Sequence Report and Contig Report pages are the web interface core structures which, together with the Text search utility and the Blast utility, allow easy access to the data stored in the database.

DECADE web portal: toward the integration of MaGa, EarthChem and VOTW data systems to further the knowledge on Earth degassing

NASA Astrophysics Data System (ADS)

Cardellini, Carlo; Frigeri, Alessandro; Lehnert, Kerstin; Ash, Jason; McCormick, Brendan; Chiodini, Giovanni; Fischer, Tobias; Cottrell, Elizabeth

2015-04-01

The release of volatiles from the Earth's interior takes place in both volcanic and non-volcanic areas of the planet. The comprehension of such complex process and the improvement of the current estimates of global carbon emissions, will greatly benefit from the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing interoperability between three data systems that will make their data accessible via the DECADE portal: (1) the Smithsonian Institutionian's Global Volcanism Program database (VOTW) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. The DECADE web portal will create a powerful search engine of these databases from a single entry point and will return comprehensive multi-component datasets. A user will be able, for example, to obtain data relating to compositions of emitted gases, compositions and age of the erupted products and coincident activity, of a specific volcano. This level of capability requires a complete synergy between the databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process allowing to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

The Footprint Database and Web Services of the Herschel Space Observatory

NASA Astrophysics Data System (ADS)

Dobos, László; Varga-Verebélyi, Erika; Verdugo, Eva; Teyssier, David; Exter, Katrina; Valtchanov, Ivan; Budavári, Tamás; Kiss, Csaba

2016-10-01

Data from the Herschel Space Observatory is freely available to the public but no uniformly processed catalogue of the observations has been published so far. To date, the Herschel Science Archive does not contain the exact sky coverage (footprint) of individual observations and supports search for measurements based on bounding circles only. Drawing on previous experience in implementing footprint databases, we built the Herschel Footprint Database and Web Services for the Herschel Space Observatory to provide efficient search capabilities for typical astronomical queries. The database was designed with the following main goals in mind: (a) provide a unified data model for meta-data of all instruments and observational modes, (b) quickly find observations covering a selected object and its neighbourhood, (c) quickly find every observation in a larger area of the sky, (d) allow for finding solar system objects crossing observation fields. As a first step, we developed a unified data model of observations of all three Herschel instruments for all pointing and instrument modes. Then, using telescope pointing information and observational meta-data, we compiled a database of footprints. As opposed to methods using pixellation of the sphere, we represent sky coverage in an exact geometric form allowing for precise area calculations. For easier handling of Herschel observation footprints with rather complex shapes, two algorithms were implemented to reduce the outline. Furthermore, a new visualisation tool to plot footprints with various spherical projections was developed. Indexing of the footprints using Hierarchical Triangular Mesh makes it possible to quickly find observations based on sky coverage, time and meta-data. The database is accessible via a web site http://herschel.vo.elte.hu and also as a set of REST web service functions, which makes it readily usable from programming environments such as Python or IDL. The web service allows downloading footprint data in various formats including Virtual Observatory standards.

The Planetary Virtual Observatory and Laboratory (PVOL) and its integration into the Virtual European Solar and Planetary Access (VESPA)

NASA Astrophysics Data System (ADS)

Hueso, R.; Juaristi, J.; Legarreta, J.; Sánchez-Lavega, A.; Rojas, J. F.; Erard, S.; Cecconi, B.; Le Sidaner, Pierre

2018-01-01

Since 2003 the Planetary Virtual Observatory and Laboratory (PVOL) has been storing and serving publicly through its web site a large database of amateur observations of the Giant Planets (Hueso et al., 2010a). These images are used for scientific research of the atmospheric dynamics and cloud structure on these planets and constitute a powerful resource to address time variable phenomena in their atmospheres. Advances over the last decade in observation techniques, and a wider recognition by professional astronomers of the quality of amateur observations, have resulted in the need to upgrade this database. We here present major advances in the PVOL database, which has evolved into a full virtual planetary observatory encompassing also observations of Mercury, Venus, Mars, the Moon and the Galilean satellites. Besides the new objects, the images can be tagged and the database allows simple and complex searches over the data. The new web service: PVOL2 is available online in http://pvol2.ehu.eus/.

EcoCyc: a comprehensive database resource for Escherichia coli

PubMed Central

Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro; Ingraham, John; Paley, Suzanne; Paulsen, Ian T.; Peralta-Gil, Martín; Karp, Peter D.

2005-01-01

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions. PMID:15608210

Patient-Oriented Cancer Information on the Internet: A Comparison of Wikipedia and a Professionally Maintained Database

PubMed Central

Rajagopalan, Malolan S.; Khanna, Vineet K.; Leiter, Yaacov; Stott, Meghan; Showalter, Timothy N.; Dicker, Adam P.; Lawrence, Yaacov R.

2011-01-01

Purpose: A wiki is a collaborative Web site, such as Wikipedia, that can be freely edited. Because of a wiki's lack of formal editorial control, we hypothesized that the content would be less complete and accurate than that of a professional peer-reviewed Web site. In this study, the coverage, accuracy, and readability of cancer information on Wikipedia were compared with those of the patient-orientated National Cancer Institute's Physician Data Query (PDQ) comprehensive cancer database. Methods: For each of 10 cancer types, medically trained personnel scored PDQ and Wikipedia articles for accuracy and presentation of controversies by using an appraisal form. Reliability was assessed by using interobserver variability and test-retest reproducibility. Readability was calculated from word and sentence length. Results: Evaluators were able to rapidly assess articles (18 minutes/article), with a test-retest reliability of 0.71 and interobserver variability of 0.53. For both Web sites, inaccuracies were rare, less than 2% of information examined. PDQ was significantly more readable than Wikipedia: Flesch-Kincaid grade level 9.6 versus 14.1. There was no difference in depth of coverage between PDQ and Wikipedia (29.9, 34.2, respectively; maximum possible score 72). Controversial aspects of cancer care were relatively poorly discussed in both resources (2.9 and 6.1 for PDQ and Wikipedia, respectively, NS; maximum possible score 18). A planned subanalysis comparing common and uncommon cancers demonstrated no difference. Conclusion: Although the wiki resource had similar accuracy and depth as the professionally edited database, it was significantly less readable. Further research is required to assess how this influences patients' understanding and retention. PMID:22211130

Web-services-based spatial decision support system to facilitate nuclear waste siting

NASA Astrophysics Data System (ADS)

Huang, L. Xinglai; Sheng, Grant

2006-10-01

The availability of spatial web services enables data sharing among managers, decision and policy makers and other stakeholders in much simpler ways than before and subsequently has created completely new opportunities in the process of spatial decision making. Though generally designed for a certain problem domain, web-services-based spatial decision support systems (WSDSS) can provide a flexible problem-solving environment to explore the decision problem, understand and refine problem definition, and generate and evaluate multiple alternatives for decision. This paper presents a new framework for the development of a web-services-based spatial decision support system. The WSDSS is comprised of distributed web services that either have their own functions or provide different geospatial data and may reside in different computers and locations. WSDSS includes six key components, namely: database management system, catalog, analysis functions and models, GIS viewers and editors, report generators, and graphical user interfaces. In this study, the architecture of a web-services-based spatial decision support system to facilitate nuclear waste siting is described as an example. The theoretical, conceptual and methodological challenges and issues associated with developing web services-based spatial decision support system are described.

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

PubMed Central

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-01-01

Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools. PMID:18021453

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

PubMed

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-11-19

Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.

The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases.

PubMed

Mostaguir, Khaled; Hoogland, Christine; Binz, Pierre-Alain; Appel, Ron D

2003-08-01

The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.

Managing Data, Provenance and Chaos through Standardization and Automation at the Georgia Coastal Ecosystems LTER Site

NASA Astrophysics Data System (ADS)

Sheldon, W.

2013-12-01

Managing data for a large, multidisciplinary research program such as a Long Term Ecological Research (LTER) site is a significant challenge, but also presents unique opportunities for data stewardship. LTER research is conducted within multiple organizational frameworks (i.e. a specific LTER site as well as the broader LTER network), and addresses both specific goals defined in an NSF proposal as well as broader goals of the network; therefore, every LTER data can be linked to rich contextual information to guide interpretation and comparison. The challenge is how to link the data to this wealth of contextual metadata. At the Georgia Coastal Ecosystems LTER we developed an integrated information management system (GCE-IMS) to manage, archive and distribute data, metadata and other research products as well as manage project logistics, administration and governance (figure 1). This system allows us to store all project information in one place, and provide dynamic links through web applications and services to ensure content is always up to date on the web as well as in data set metadata. The database model supports tracking changes over time in personnel roles, projects and governance decisions, allowing these databases to serve as canonical sources of project history. Storing project information in a central database has also allowed us to standardize both the formatting and content of critical project information, including personnel names, roles, keywords, place names, attribute names, units, and instrumentation, providing consistency and improving data and metadata comparability. Lookup services for these standard terms also simplify data entry in web and database interfaces. We have also coupled the GCE-IMS to our MATLAB- and Python-based data processing tools (i.e. through database connections) to automate metadata generation and packaging of tabular and GIS data products for distribution. Data processing history is automatically tracked throughout the data lifecycle, from initial import through quality control, revision and integration by our data processing system (GCE Data Toolbox for MATLAB), and included in metadata for versioned data products. This high level of automation and system integration has proven very effective in managing the chaos and scalability of our information management program.

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

HC Forum®: a web site based on an international human cytogenetic database

PubMed Central

Cohen, Olivier; Mermet, Marie-Ange; Demongeot, Jacques

2001-01-01

Familial structural rearrangements of chromosomes represent a factor of malformation risk that could vary over a large range, making genetic counseling difficult. However, they also represent a powerful tool for increasing knowledge of the genome, particularly by studying breakpoints and viable imbalances of the genome. We have developed a collaborative database that now includes data on more than 4100 families, from which we have developed a web site called HC Forum® (http://HCForum.imag.fr). It offers geneticists assistance in diagnosis and in genetic counseling by assessing the malformation risk with statistical models. For researchers, interactive interfaces exhibit the distribution of chromosomal breakpoints and of the genome regions observed at birth in trisomy or in monosomy. Dedicated tools including an interactive pedigree allow electronic submission of data, which will be anonymously shown in a forum for discussions. After validation, data are definitively registered in the database with the email of the sender, allowing direct location of biological material. Thus HC Forum® constitutes a link between diagnosis laboratories and genome research centers, and after 1 year, more than 700 users from about 40 different countries already exist. PMID:11125121

Possible costs associated with investigating and mitigating geologic hazards in rural areas of western San Mateo County, California with a section on using the USGS website to determine the cost of developing property for residences in rural parts of San Mateo County, California

USGS Publications Warehouse

Brabb, Earl E.; Roberts, Sebastian; Cotton, William R.; Kropp, Alan L.; Wright, Robert H.; Zinn, Erik N.; Digital database by Roberts, Sebastian; Mills, Suzanne K.; Barnes, Jason B.; Marsolek, Joanna E.

2000-01-01

This publication consists of a digital map database on a geohazards web site, http://kaibab.wr.usgs.gov/geohazweb/intro.htm, this text, and 43 digital map images available for downloading at this site. The report is stored as several digital files, in ARC export (uncompressed) format for the database, and Postscript and PDF formats for the map images. Several of the source data layers for the images have already been released in other publications by the USGS and are available for downloading on the Internet. These source layers are not included in this digital database, but rather a reference is given for the web site where the data can be found in digital format. The exported ARC coverages and grids lie in UTM zone 10 projection. The pamphlet, which only describes the content and character of the digital map database, is included as Postscript, PDF, and ASCII text files and is also available on paper as USGS Open-File Report 00-127. The full versatility of the spatial database is realized by importing the ARC export files into ARC/INFO or an equivalent GIS. Other GIS packages, including MapInfo and ARCVIEW, can also use the ARC export files. The Postscript map image can be used for viewing or plotting in computer systems with sufficient capacity, and the considerably smaller PDF image files can be viewed or plotted in full or in part from Adobe ACROBAT software running on Macintosh, PC, or UNIX platforms.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

NASA Astrophysics Data System (ADS)

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

PubMed

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

Database-driven web interface automating gyrokinetic simulations for validation

NASA Astrophysics Data System (ADS)

Ernst, D. R.

2010-11-01

We are developing a web interface to connect plasma microturbulence simulation codes with experimental data. The website automates the preparation of gyrokinetic simulations utilizing plasma profile and magnetic equilibrium data from TRANSP analysis of experiments, read from MDSPLUS over the internet. This database-driven tool saves user sessions, allowing searches of previous simulations, which can be restored to repeat the same analysis for a new discharge. The website includes a multi-tab, multi-frame, publication quality java plotter Webgraph, developed as part of this project. Input files can be uploaded as templates and edited with context-sensitive help. The website creates inputs for GS2 and GYRO using a well-tested and verified back-end, in use for several years for the GS2 code [D. R. Ernst et al., Phys. Plasmas 11(5) 2637 (2004)]. A centralized web site has the advantage that users receive bug fixes instantaneously, while avoiding the duplicated effort of local compilations. Possible extensions to the database to manage run outputs, toward prototyping for the Fusion Simulation Project, are envisioned. Much of the web development utilized support from the DoE National Undergraduate Fellowship program [e.g., A. Suarez and D. R. Ernst, http://meetings.aps.org/link/BAPS.2005.DPP.GP1.57.

TREATABILITY DATABASE FOR DRINKING WATER CHEMICALS (CCL)

EPA Science Inventory

The Treatability Data Base will assemble referenced data on the control of contaminants in drinking water. It will be an interactive data base, housed in an EPA, web-accessible site. It may be used for many purposes, including: identifying an effective treatment process or a se...

49 CFR 192.949 - How does an operator notify PHMSA?

Code of Federal Regulations, 2013 CFR

2013-10-01

... MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF... Materials Safety Administration, U.S. Department of Transportation, Information Resources Manager, PHP-10... Management Database (IMDB) Web site at http://primis.rspa.dot.gov/gasimp/. [68 FR 69817, Dec. 15, 2003, as...

49 CFR 192.949 - How does an operator notify PHMSA?

Code of Federal Regulations, 2014 CFR

2014-10-01

... MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF... Materials Safety Administration, U.S. Department of Transportation, Information Resources Manager, PHP-10... Management Database (IMDB) Web site at http://primis.rspa.dot.gov/gasimp/. [68 FR 69817, Dec. 15, 2003, as...

49 CFR 192.949 - How does an operator notify PHMSA?

Code of Federal Regulations, 2012 CFR

2012-10-01

... MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF... Materials Safety Administration, U.S. Department of Transportation, Information Resources Manager, PHP-10... Management Database (IMDB) Web site at http://primis.rspa.dot.gov/gasimp/. [68 FR 69817, Dec. 15, 2003, as...

49 CFR 192.949 - How does an operator notify PHMSA?

Code of Federal Regulations, 2011 CFR

2011-10-01

... MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF... Materials Safety Administration, U.S. Department of Transportation, Information Resources Manager, PHP-10... Management Database (IMDB) Web site at http://primis.rspa.dot.gov/gasimp/. [68 FR 69817, Dec. 15, 2003, as...

Cleanups In My Community (CIMC) - Recovery Act Funded Cleanups, National Layer

EPA Pesticide Factsheets

This data layer provides access to Recovery Act Funded Cleanup sites as part of the CIMC web service. The American Recovery and Reinvestment Act was signed into law by President Obama on February 17th, 2009 and all reporting on ARRA for these 3 programs was complete as of 2013. Out of the five EPA programs that distributed recovery act funding, three of them were cleanup programs: Brownfields, Superfund and Leaking Underground Storage Tanks. CIMC provides information on site cleanups that received ARRA Recovery Act funding for Superfund and Brownfields, but not Leaking Underground Storage Tanks. Data for Brownfields came from the ACRES database. Data for Superfund came from the Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) database. Data in CIMC no longer need to be updated for the ARRA program. For information on all EPA Recovery Act funded work, please see: http://archive.epa.gov/recovery/web/html/ and http://epamap17.epa.gov/arra/.

A Tactical Framework for Cyberspace Situational Awareness

DTIC Science & Technology

2010-06-01

Command & Control 1. VOIP Telephone 2. Internet Chat 3. Web App ( TBMCS ) 4. Email 5. Web App (PEX) 6. Database (CAMS) 7. Database (ARMS) 8...Database (LogMod) 9. Resource (WWW) 10. Application (PFPS) Mission Planning 1. Application (PFPS) 2. Email 3. Web App ( TBMCS ) 4. Internet Chat...1. Web App (PEX) 2. Database (ARMS) 3. Web App ( TBMCS ) 4. Email 5. Database (CAMS) 6. VOIP Telephone 7. Application (PFPS) 8. Internet Chat 9

Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF)

PubMed Central

Gupta, Amarnath; Bug, William; Marenco, Luis; Qian, Xufei; Condit, Christopher; Rangarajan, Arun; Müller, Hans Michael; Miller, Perry L.; Sanders, Brian; Grethe, Jeffrey S.; Astakhov, Vadim; Shepherd, Gordon; Sternberg, Paul W.; Martone, Maryann E.

2009-01-01

The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov. PMID:18958629

Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF).

PubMed

Gupta, Amarnath; Bug, William; Marenco, Luis; Qian, Xufei; Condit, Christopher; Rangarajan, Arun; Müller, Hans Michael; Miller, Perry L; Sanders, Brian; Grethe, Jeffrey S; Astakhov, Vadim; Shepherd, Gordon; Sternberg, Paul W; Martone, Maryann E

2008-09-01

The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov.

VKCDB: voltage-gated K+ channel database updated and upgraded.

PubMed

Gallin, Warren J; Boutet, Patrick A

2011-01-01

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data

PubMed Central

Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

2008-01-01

The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org. PMID:17932055

Satellite Communications Technology Database. Part 2

NASA Technical Reports Server (NTRS)

2001-01-01

The Satellite Communications Technology Database is a compilation of data on state-of-the-art Ka-band technologies current as of January 2000. Most U.S. organizations have not published much of their Ka-band technology data, and so the great majority of this data is drawn largely from Japanese, European, and Canadian publications and Web sites. The data covers antennas, high power amplifiers, low noise amplifiers, MMIC devices, microwave/IF switch matrices, SAW devices, ASIC devices, power and data storage. The data herein is raw, and is often presented simply as the download of a table or figure from a site, showing specified technical characteristics, with no further explanation.

Wiki use in mental health practice: recognizing potential use of collaborative technology.

PubMed

Bastida, Richard; McGrath, Ian; Maude, Phil

2010-04-01

Web 2.0, the second-generation of the World Wide Web, differs to earlier versions of Web development and design in that it facilitates more user-friendly, interactive information sharing and mechanisms for greater collaboration between users. Examples of Web 2.0 include Web-based communities, hosted services, social networking sites, video sharing sites, blogs, mashups, and wikis. Users are able to interact with others across the world or to add to or change website content. This paper examines examples of wiki use in the Australian mental health sector. A wiki can be described as an online collaborative and interactive database that can be easily edited by users. They are accessed via a standard Web browser which has an interface similar to traditional Web pages, thus do not require special application or software for the user. Although there is a paucity of literature describing wiki use in mental health, other industries have developed uses, including a repository of knowledge, a platform for collaborative writing, a project management tool, and an alternative to traditional Web pages or Intranets. This paper discusses the application of wikis in other industries and offers suggestions by way of examples of how this technology could be used in the mental health sector.

LymPHOS 2.0: an update of a phosphosite database of primary human T cells

PubMed Central

Nguyen, Tien Dung; Vidal-Cortes, Oriol; Gallardo, Oscar; Abian, Joaquin; Carrascal, Montserrat

2015-01-01

LymPHOS is a web-oriented database containing peptide and protein sequences and spectrometric information on the phosphoproteome of primary human T-Lymphocytes. Current release 2.0 contains 15 566 phosphorylation sites from 8273 unique phosphopeptides and 4937 proteins, which correspond to a 45-fold increase over the original database description. It now includes quantitative data on phosphorylation changes after time-dependent treatment with activators of the TCR-mediated signal transduction pathway. Sequence data quality has also been improved with the use of multiple search engines for database searching. LymPHOS can be publicly accessed at http://www.lymphos.org. Database URL: http://www.lymphos.org. PMID:26708986

Drug-Path: a database for drug-induced pathways.

PubMed

Zeng, Hui; Qiu, Chengxiang; Cui, Qinghua

2015-01-01

Some databases for drug-associated pathways have been built and are publicly available. However, the pathways curated in most of these databases are drug-action or drug-metabolism pathways. In recent years, high-throughput technologies such as microarray and RNA-sequencing have produced lots of drug-induced gene expression profiles. Interestingly, drug-induced gene expression profile frequently show distinct patterns, indicating that drugs normally induce the activation or repression of distinct pathways. Therefore, these pathways contribute to study the mechanisms of drugs and drug-repurposing. Here, we present Drug-Path, a database of drug-induced pathways, which was generated by KEGG pathway enrichment analysis for drug-induced upregulated genes and downregulated genes based on drug-induced gene expression datasets in Connectivity Map. Drug-Path provides user-friendly interfaces to retrieve, visualize and download the drug-induced pathway data in the database. In addition, the genes deregulated by a given drug are highlighted in the pathways. All data were organized using SQLite. The web site was implemented using Django, a Python web framework. Finally, we believe that this database will be useful for related researches. © The Author(s) 2015. Published by Oxford University Press.

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

Database resources of the National Center for Biotechnology Information.

PubMed

Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

2007-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene; Ye, Jian

2009-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

KernPaeP - a web-based pediatric palliative documentation system for home care.

PubMed

Hartz, Tobias; Verst, Hendrik; Ueckert, Frank

2009-01-01

KernPaeP is a new web-based on- and offline documentation system, which has been developed for pediatric palliative care-teams supporting patient documentation and communication among health care professionals. It provides a reliable system making fast and secure home care documentation possible. KernPaeP is accessible online by registered users using any web-browser. Home care teams use an offline version of KernPaeP running on a netbook for patient documentation on site. Identifying and medical patient data are strictly separated and stored on two database servers. The system offers a stable, enhanced two-way algorithm for synchronization between the offline component and the central database servers. KernPaeP is implemented meeting highest security standards while still maintaining high usability. The web-based documentation system allows ubiquitous and immediate access to patient data. Sumptuous paper work is replaced by secure and comprehensive electronic documentation. KernPaeP helps saving time and improving the quality of documentation. Due to development in close cooperation with pediatric palliative professionals, KernPaeP fulfils the broad needs of home-care documentation. The technique of web-based online and offline documentation is in general applicable for arbitrary home care scenarios.

ENVIRONMENTAL EFFECTS OF DREDGING AND DISPOSAL (E2-D2)

EPA Science Inventory

US Army Corps of Engineers public web site for the "Environmental Effects of Dredging and Disposal" ("E2-D2") searchable database of published reports and studies about environmental impacts associated with dredging and disposal operations. Many of the reports and studies are ava...

Scale-Independent Relational Query Processing

ERIC Educational Resources Information Center

Armbrust, Michael Paul

2013-01-01

An increasingly common pattern is for newly-released web applications to succumb to a "Success Disaster". In this scenario, overloaded database machines and resultant high response times destroy a previously good user experience, just as a site is becoming popular. Unfortunately, the data independence provided by a traditional relational…

Internet Resources for Civic Educators. ERIC Digest.

ERIC Educational Resources Information Center

Pinhey, Laura A.

The Internet is an important resource for K-12 citizenship education teachers. Curriculum guides, lesson plans, government documents, conference proceedings, databases, photographs, and multimedia files provide the classroom teacher with a variety of materials including many primary sources. An annotated list of 15 World Wide Web sites are…

Remote vibration monitoring system using wireless internet data transfer

NASA Astrophysics Data System (ADS)

Lemke, John

2000-06-01

Vibrations from construction activities can affect infrastructure projects in several ways. Within the general vicinity of a construction site, vibrations can result in damage to existing structures, disturbance to people, damage to sensitive machinery, and degraded performance of precision instrumentation or motion sensitive equipment. Current practice for monitoring vibrations in the vicinity of construction sites commonly consists of measuring free field or structural motions using velocity transducers connected to a portable data acquisition unit via cables. This paper describes an innovative way to collect, process, transmit, and analyze vibration measurements obtained at construction sites. The system described measures vibration at the sensor location, performs necessary signal conditioning and digitization, and sends data to a Web server using wireless data transmission and Internet protocols. A Servlet program running on the Web server accepts the transmitted data and incorporates it into a project database. Two-way interaction between the Web-client and the Web server is accomplished through the use of a Servlet program and a Java Applet running inside a browser located on the Web client's computer. Advantages of this system over conventional vibration data logging systems include continuous unattended monitoring, reduced costs associated with field data collection, instant access to data files and graphs by project team members, and the ability to remotely modify data sampling schemes.

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.

PubMed

Picardi, Ernesto; D'Antonio, Mattia; Carrabino, Danilo; Castrignanò, Tiziana; Pesole, Graziano

2011-05-01

ExpEdit is a web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments. Mapping data (in SAM/BAM format) or directly sequence reads [in FASTQ/short read archive (SRA) format] can be provided as input to carry out a comparative analysis against a large collection of known editing sites collected in DARNED database as well as other user-provided potentially edited positions. Results are shown as dynamic tables containing University of California, Santa Cruz (UCSC) links for a quick examination of the genomic context. ExpEdit is freely available on the web at http://www.caspur.it/ExpEdit/.

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

Accounting Data to Web Interface Using PERL

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

Hargeaves, C

2001-08-13

This document will explain the process to create a web interface for the accounting information generated by the High Performance Storage Systems (HPSS) accounting report feature. The accounting report contains useful data but it is not easily accessed in a meaningful way. The accounting report is the only way to see summarized storage usage information. The first step is to take the accounting data, make it meaningful and store the modified data in persistent databases. The second step is to generate the various user interfaces, HTML pages, that will be used to access the data. The third step is tomore » transfer all required files to the web server. The web pages pass parameters to Common Gateway Interface (CGI) scripts that generate dynamic web pages and graphs. The end result is a web page with specific information presented in text with or without graphs. The accounting report has a specific format that allows the use of regular expressions to verify if a line is storage data. Each storage data line is stored in a detailed database file with a name that includes the run date. The detailed database is used to create a summarized database file that also uses run date in its name. The summarized database is used to create the group.html web page that includes a list of all storage users. Scripts that query the database folder to build a list of available databases generate two additional web pages. A master script that is run monthly as part of a cron job, after the accounting report has completed, manages all of these individual scripts. All scripts are written in the PERL programming language. Whenever possible data manipulation scripts are written as filters. All scripts are written to be single source, which means they will function properly on both the open and closed networks at LLNL. The master script handles the command line inputs for all scripts, file transfers to the web server and records run information in a log file. The rest of the scripts manipulate the accounting data or use the files created to generate HTML pages. Each script will be described in detail herein. The following is a brief description of HPSS taken directly from an HPSS web site. ''HPSS is a major development project, which began in 1993 as a Cooperative Research and Development Agreement (CRADA) between government and industry. The primary objective of HPSS is to move very large data objects between high performance computers, workstation clusters, and storage libraries at speeds many times faster than is possible with today's software systems. For example, HPSS can manage parallel data transfers from multiple network-connected disk arrays at rates greater than 1 Gbyte per second, making it possible to access high definition digitized video in real time.'' The HPSS accounting report is a canned report whose format is controlled by the HPSS developers.« less

49 CFR 575.106 - Tire fuel efficiency consumer information program.

Code of Federal Regulations, 2013 CFR

2013-10-01

... tires, deep tread, winter-type snow tires, space-saver or temporary use spare tires, tires with nominal... deep tread, winter-type snow tires and limited production tires that it manufactures which are exempt... to have included in the database of information available to consumers on NHTSA's Web site. (ii...

49 CFR 575.106 - Tire fuel efficiency consumer information program.

Code of Federal Regulations, 2014 CFR

2014-10-01

... tires, deep tread, winter-type snow tires, space-saver or temporary use spare tires, tires with nominal... deep tread, winter-type snow tires and limited production tires that it manufactures which are exempt... to have included in the database of information available to consumers on NHTSA's Web site. (ii...

49 CFR 575.106 - Tire fuel efficiency consumer information program.

Code of Federal Regulations, 2012 CFR

2012-10-01

... tires, deep tread, winter-type snow tires, space-saver or temporary use spare tires, tires with nominal... deep tread, winter-type snow tires and limited production tires that it manufactures which are exempt... to have included in the database of information available to consumers on NHTSA's Web site. (ii...

Blending Technology with Camp Tradition: Technology Can Simplify Camp Operations.

ERIC Educational Resources Information Center

Salzman, Jeff

2000-01-01

Discusses uses of technology appropriate for camps, which are service organizations based on building relationships. Describes relationship marketing and how it can be enhanced through use of Web sites, interactive brochures, and client databases. Outlines other technology uses at camp: automated dispensing of medications, satellite tracking of…

Native American Youth and Culturally Sensitive Interventions: A Systematic Review

ERIC Educational Resources Information Center

Jackson, Kelly F.; Hodge, David R.

2010-01-01

Objective: A systematic evaluation of the effectiveness of culturally sensitive interventions (CSIs) with Native American youth was conducted. Method: Electronic bibliographic databases, Web sites, and manual searches were used to identify 11 outcome studies that examined CSI effectiveness with Native American youth. Results: This review found…

Circ's Up, Budgets Leap

ERIC Educational Resources Information Center

Hoffert, Barbara

2007-01-01

From the ascendance of the reference database and web sites offering endless opportunities for cyber-promotion to the crowds swarming through the doors to avail themselves of new computers, the Internet has transformed the way public libraries do business. That is not news. What is exciting, though, is how the Internet continues to change public…

The Embedded Librarian Program

ERIC Educational Resources Information Center

Matthew, Victoria; Schroeder, Ann

2006-01-01

With the huge increase in online learning at colleges around the country, libraries need to consider how to serve the growing contingent of online students. Some typical library services include a Web site, remote access to databases, e-mail assistance, a toll-free phone number, a procedure for supplying library materials to students, FAQs,…

Consortial IT Services: Collaborating To Reduce the Pain.

ERIC Educational Resources Information Center

Klonoski, Ed

The Connecticut Distance Learning Consortium (CTDLC) provides its 32 members with Information Technologies (IT) services including a portal Web site, course management software, course hosting and development, faculty training, a help desk, online assessment, and a student financial aid database. These services are supplied to two- and four-year…

Database for earthquake strong motion studies in Italy

USGS Publications Warehouse

Scasserra, G.; Stewart, J.P.; Kayen, R.E.; Lanzo, G.

2009-01-01

We describe an Italian database of strong ground motion recordings and databanks delineating conditions at the instrument sites and characteristics of the seismic sources. The strong motion database consists of 247 corrected recordings from 89 earthquakes and 101 recording stations. Uncorrected recordings were drawn from public web sites and processed on a record-by-record basis using a procedure utilized in the Next-Generation Attenuation (NGA) project to remove instrument resonances, minimize noise effects through low- and high-pass filtering, and baseline correction. The number of available uncorrected recordings was reduced by 52% (mostly because of s-triggers) to arrive at the 247 recordings in the database. The site databank includes for every recording site the surface geology, a measurement or estimate of average shear wave velocity in the upper 30 m (Vs30), and information on instrument housing. Of the 89 sites, 39 have on-site velocity measurements (17 of which were performed as part of this study using SASW techniques). For remaining sites, we estimate Vs30 based on measurements on similar geologic conditions where available. Where no local velocity measurements are available, correlations with surface geology are used. Source parameters are drawn from databanks maintained (and recently updated) by Istituto Nazionale di Geofisica e Vulcanologia and include hypocenter location and magnitude for small events (M< ??? 5.5) and finite source parameters for larger events. ?? 2009 A.S. Elnashai & N.N. Ambraseys.

Molecular signatures database (MSigDB) 3.0.

PubMed

Liberzon, Arthur; Subramanian, Aravind; Pinchback, Reid; Thorvaldsdóttir, Helga; Tamayo, Pablo; Mesirov, Jill P

2011-06-15

Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.

IAU MDC Photographic Meteor Orbits Database: Version 2013

NASA Astrophysics Data System (ADS)

Neslušan, L.; Porubčan, V.; Svoreň, J.

2014-05-01

A new 2013 version of the IAU MDC photographic meteor orbits database which is an upgrade of the current 2003 version (Lindblad et al. 2003, EMP 93:249-260) is presented. To the 2003 version additional 292 orbits are added, thus the new version of the database consists of 4,873 meteors with their geophysical and orbital parameters compiled in 41 catalogues. For storing the data, a new format enabling a more simple treatment with the parameters, including the errors of their determination is applied. The data can be downloaded from the IAU MDC web site: http://www.astro.sk/IAUMDC/Ph2013/

BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska

NASA Astrophysics Data System (ADS)

Cody, R. P.; Kassin, A.; Gaylord, A. G.; Tweedie, C. E.

2013-12-01

In 2013, the Barrow Area Information Database (BAID, www.baid.utep.edu) project resumed field operations in Barrow, AK. The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 11,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Highlights for the 2013 season include the addition of more than 2000 additional research sites, providing differential global position system (dGPS) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal, deployment of a wireless sensor network, and substantial upgrades to the BAID website and web mapping applications.

NGL Viewer: a web application for molecular visualization.

PubMed

Rose, Alexander S; Hildebrand, Peter W

2015-07-01

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. 'cartoon, spacefill, licorice'). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Secure web book to store structural genomics research data.

PubMed

Manjasetty, Babu A; Höppner, Klaus; Mueller, Uwe; Heinemann, Udo

2003-01-01

Recently established collaborative structural genomics programs aim at significantly accelerating the crystal structure analysis of proteins. These large-scale projects require efficient data management systems to ensure seamless collaboration between different groups of scientists working towards the same goal. Within the Berlin-based Protein Structure Factory, the synchrotron X-ray data collection and the subsequent crystal structure analysis tasks are located at BESSY, a third-generation synchrotron source. To organize file-based communication and data transfer at the BESSY site of the Protein Structure Factory, we have developed the web-based BCLIMS, the BESSY Crystallography Laboratory Information Management System. BCLIMS is a relational data management system which is powered by MySQL as the database engine and Apache HTTP as the web server. The database interface routines are written in Python programing language. The software is freely available to academic users. Here we describe the storage, retrieval and manipulation of laboratory information, mainly pertaining to the synchrotron X-ray diffraction experiments and the subsequent protein structure analysis, using BCLIMS.

Online interactive U.S. Reservoir Sedimentation Survey Database

USGS Publications Warehouse

Gray, J.B.; Bernard, J.M.; Schwarz, G.E.; Stewart, D.W.; Ray, K.T.

2009-01-01

In April 2009, the U.S. Geological Survey and the Natural Resources Conservation Service (prior to 1994, the Soil Conservation Service) created the Reservoir Sedimentation Survey Database (RESSED) and Web site, the most comprehensive compilation of data from reservoir bathymetric and dry basin surveys in the United States. RESSED data can be useful for a number of purposes, including calculating changes in reservoir storage characteristics, quantifying rates of sediment delivery to reservoirs, and estimating erosion rates in a reservoir's watershed.

RTECS database (on the internet). Online data

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

NONE

The Registry of Toxic Effects of Chemical Substances (RTECS (trademark)) is a database of toxicological information compiled, maintained, and updated by the National Institute for Occupational Safety and Health. The program is mandated by the Occupational Safety and Health Act of 1970. The original edition, known as the `Toxic Substances List,` was published on June 28, 1971, and included toxicologic data for approximately 5,000 chemicals. Since that time, the list has continuously grown and been updated, and its name changed to the current title, `Registry of Toxic Effects of Chemical Substances.` RTECS (trademark) now contains over 133,000 chemicals as NIOSHmore » strives to fulfill the mandate to list `all known toxic substances...and the concentrations at which...toxicity is known to occur.` This database is now available for searching through the Gov. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

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

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

PubMed

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

2012-05-01

MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

Just-in-time Database-Driven Web Applications

PubMed Central

2003-01-01

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program. PMID:14517109

Standardized description of scientific evidence using the Evidence Ontology (ECO)

PubMed Central

Chibucos, Marcus C.; Mungall, Christopher J.; Balakrishnan, Rama; Christie, Karen R.; Huntley, Rachael P.; White, Owen; Blake, Judith A.; Lewis, Suzanna E.; Giglio, Michelle

2014-01-01

The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org PMID:25052702

DECADE Web Portal: Integrating MaGa, EarthChem and GVP Will Further Our Knowledge on Earth Degassing

NASA Astrophysics Data System (ADS)

Cardellini, C.; Frigeri, A.; Lehnert, K. A.; Ash, J.; McCormick, B.; Chiodini, G.; Fischer, T. P.; Cottrell, E.

2014-12-01

The release of gases from the Earth's interior to the exosphere takes place in both volcanic and non-volcanic areas of the planet. Fully understanding this complex process requires the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. We are developing interoperability between three of those, which will support more powerful synoptic studies of degassing. The three data systems that will make their data accessible via the DECADE portal are: (1) the Smithsonian Institution's Global Volcanism Program database (GVP) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. These databases are developed and maintained by institutions or groups of experts in a specific field, and data are archived in formats specific to these databases. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing a web portal that will create a powerful search engine of these databases from a single entry point. The portal will return comprehensive multi-component datasets, based on the search criteria selected by the user. For example, a single geographic or temporal search will return data relating to compositions of emitted gases and erupted products, the age of the erupted products, and coincident activity at the volcano. The development of this level of capability for the DECADE Portal requires complete synergy between these databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process. Other data systems can be easily plugged in using the existing framework. Our vision is to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

...: Notice of Public Web Conferences AGENCY: Consumer Product Safety Commission. ACTION: Notice. SUMMARY: The Consumer Product Safety Commission (``Commission,'' ``CPSC,'' or ``we'') is announcing two Web conferences... database (``Database''). The Web conferences will be webcast live from the Commission's headquarters in...

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2011-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

What Trends Do Turkish Biology Education Studies Indicate?

ERIC Educational Resources Information Center

Topsakal, Unsal Umdu; Calik, Muammer; Cavus, Ragip

2012-01-01

The aim of this study is to determine what trends Turkish biology education studies indicate. To achieve this aim, the researchers examined online databases of the Higher Education Council and open access archives of graduate theses in web sites of Turkish universities. Finally, totally 138 graduate theses were elicited to analyze in regard to…

Locating Vocational Education Curriculum and Instructional Materials. ERIC Digest.

ERIC Educational Resources Information Center

Wagner, Judith O.

This digest provides a variety of sources for vocational education curricula, lesson plans, and other instructional materials. The section on networking includes listservs and World Wide Web sites that lead to curriculum resources and other valuable information. Access points to the ERIC database are listed, as are instructional materials labs and…

The availability of web sites offering to sell opioid medications without prescriptions.

PubMed

Forman, Robert F; Woody, George E; McLellan, Thomas; Lynch, Kevin G

2006-07-01

This study was designed to determine the availability of web sites offering to sell opioid medications without prescriptions. Forty-seven Internet searches were conducted with a variety of opioid medication terms, including "codeine," "no prescription Vicodin," and "OxyContin." Two independent raters examined the links generated in each search and resolved any coding disagreements. The resulting links were coded as "no prescription web sites" (NPWs) if they offered to sell opioid medications without prescriptions. In searches with terms such as "no prescription codeine" and "Vicodin," over 50% of the links obtained were coded as "NPWs." The proportion of links yielding NPWs was greater when the phrase "no prescription" was added to the opioid term. More than 300 opioid NPWs were identified and entered into a database. Three national drug-use monitoring studies have cited significant increases in prescription opioid use over the past 5 years, particularly among young people. The emergence of NPWs introduces a new vector for unregulated access to opioids. Research is needed to determine the effect of NPWs on prescription opioid use initiation, misuse, and dependence.

Web-Based Satellite Products Database for Meteorological and Climate Applications

NASA Technical Reports Server (NTRS)

Phan, Dung; Spangenberg, Douglas A.; Palikonda, Rabindra; Khaiyer, Mandana M.; Nordeen, Michele L.; Nguyen, Louis; Minnis, Patrick

2004-01-01

The need for ready access to satellite data and associated physical parameters such as cloud properties has been steadily growing. Air traffic management, weather forecasters, energy producers, and weather and climate researchers among others can utilize more satellite information than in the past. Thus, it is essential that such data are made available in near real-time and as archival products in an easy-access and user friendly environment. A host of Internet web sites currently provide a variety of satellite products for various applications. Each site has a unique contribution with appeal to a particular segment of the public and scientific community. This is no less true for the NASA Langley's Clouds and Radiation (NLCR) website (http://www-pm.larc.nasa.gov) that has been evolving over the past 10 years to support a variety of research projects This website was originally developed to display cloud products derived from the Geostationary Operational Environmental Satellite (GOES) over the Southern Great Plains for the Atmospheric Radiation Measurement (ARM) Program. It has evolved into a site providing a comprehensive database of near real-time and historical satellite products used for meteorological, aviation, and climate studies. To encourage the user community to take advantage of the site, this paper summarizes the various products and projects supported by the website and discusses future options for new datasets.

The strategies WDK: a graphical search interface and web development kit for functional genomics databases

PubMed Central

Fischer, Steve; Aurrecoechea, Cristina; Brunk, Brian P.; Gao, Xin; Harb, Omar S.; Kraemer, Eileen T.; Pennington, Cary; Treatman, Charles; Kissinger, Jessica C.; Roos, David S.; Stoeckert, Christian J.

2011-01-01

Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy’s flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org PMID:21705364

USGS Nonindigenous Aquatic Species database with a focus on the introduced fishes of the lower Tennessee and Cumberland drainages

USGS Publications Warehouse

Fuller, Pamela L.; Cannister, Matthew; Johansen, Rebecca; Estes, L. Dwayne; Hamilton, Steven W.; Barrass, Andrew N.

2013-01-01

The Nonindigenous Aquatic Species (NAS) database (http://nas.er.usgs.gov) functions as a national repository and clearinghouse for occurrence data for introduced species within the United States. Included is locality information on over 1,100 species of vertebrates, invertebrates, and vascular plants introduced as early as 1850. Taxa include foreign (exotic) species and species native to North America that have been transported outside of their natural range. Locality data are obtained from published and unpublished literature, state, federal and local monitoring programs, museum accessions, on-line databases, websites, professional communications and on-line reporting forms. The NAS web site provides immediate access to new occurrence records through a real-time interface with the NAS database. Visitors to the web site are presented with a set of pre-defined queries that generate lists of species according to state or hydrologic basin of interest. Fact sheets, distribution maps, and information on new occurrences are updated as new records and information become available. The NAS database allows resource managers to learn of new introductions reported in their region or nearby regions, improving response time. Conversely, managers are encouraged to report their observations of new occurrences to the NAS database so information can be disseminated to other managers, researchers, and the public. In May 2004, the NAS database incorporated an Alert System to notify registered users of new introductions as part of a national early detection/rapid response system. Users can register to receive alerts based on geographic or taxonomic criteria. The NAS database was used to identify 23 fish species introduced into the lower Tennessee and Cumberland drainages. Most of these are sport fish stocked to support fisheries, but the list also includes accidental and illegal introductions such as Asian Carps, clupeids, various species popular in the aquarium trade, and Atlantic Needlefish (Strongylura marina) that was introduced via the newly-constructed Tennessee-Tombigbee Canal.

Alternatives to animal testing: information resources via the Internet and World Wide Web.

PubMed

Hakkinen, P J Bert; Green, Dianne K

2002-04-25

Many countries, including the United States, Canada, European Union member states, and others, require that a comprehensive search for possible alternatives be completed before beginning some or all research involving animals. Completing comprehensive alternatives searches and keeping current with information associated with alternatives to animal testing is a challenge that will be made easier as people throughout the world gain access to the Internet and World Wide Web. Numerous Internet and World Wide Web resources are available to provide guidance and other information on in vitro and other alternatives to animal testing. A comprehensive Web site is Alternatives to Animal Testing on the Web (Altweb), which serves as an online clearinghouse for resources, information, and news about alternatives to animal testing. Examples of other important Web sites include the joint one for the (US) Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) and the National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM) and the Norwegian Reference Centre for Laboratory Animal Science and Alternatives (The NORINA database). Internet mailing lists and online access to bulletin boards, discussion areas, newsletters, and journals are other ways to access and share information to stay current with alternatives to animal testing.

Casimage project: a digital teaching files authoring environment.

PubMed

Rosset, Antoine; Muller, Henning; Martins, Martina; Dfouni, Natalia; Vallée, Jean-Paul; Ratib, Osman

2004-04-01

The goal of the Casimage project is to offer an authoring and editing environment integrated with the Picture Archiving and Communication Systems (PACS) for creating image-based electronic teaching files. This software is based on a client/server architecture allowing remote access of users to a central database. This authoring environment allows radiologists to create reference databases and collection of digital images for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The environment includes all tools to create teaching files, including textual description, annotations, and image manipulation. The software also allows users to generate stand-alone CD-ROMs and web-based teaching files to easily share their collections. The system includes a web server compatible with the Medical Imaging Resource Center standard (MIRC, http://mirc.rsna.org) to easily integrate collections in the RSNA web network dedicated to teaching files. This software could be installed on any PACS workstation to allow users to add new cases at any time and anywhere during clinical operations. Several images collections were created with this tool, including thoracic imaging that was subsequently made available on a CD-Rom and on our web site and through the MIRC network for public access.

Landslide databases for applied landslide impact research: the example of the landslide database for the Federal Republic of Germany

NASA Astrophysics Data System (ADS)

Damm, Bodo; Klose, Martin

2014-05-01

This contribution presents an initiative to develop a national landslide database for the Federal Republic of Germany. It highlights structure and contents of the landslide database and outlines its major data sources and the strategy of information retrieval. Furthermore, the contribution exemplifies the database potentials in applied landslide impact research, including statistics of landslide damage, repair, and mitigation. The landslide database offers due to systematic regional data compilation a differentiated data pool of more than 5,000 data sets and over 13,000 single data files. It dates back to 1137 AD and covers landslide sites throughout Germany. In seven main data blocks, the landslide database stores besides information on landslide types, dimensions, and processes, additional data on soil and bedrock properties, geomorphometry, and climatic or other major triggering events. A peculiarity of this landslide database is its storage of data sets on land use effects, damage impacts, hazard mitigation, and landslide costs. Compilation of landslide data is based on a two-tier strategy of data collection. The first step of information retrieval includes systematic web content mining and exploration of online archives of emergency agencies, fire and police departments, and news organizations. Using web and RSS feeds and soon also a focused web crawler, this enables effective nationwide data collection for recent landslides. On the basis of this information, in-depth data mining is performed to deepen and diversify the data pool in key landslide areas. This enables to gather detailed landslide information from, amongst others, agency records, geotechnical reports, climate statistics, maps, and satellite imagery. Landslide data is extracted from these information sources using a mix of methods, including statistical techniques, imagery analysis, and qualitative text interpretation. The landslide database is currently migrated to a spatial database system running on PostgreSQL/PostGIS. This provides advanced functionality for spatial data analysis and forms the basis for future data provision and visualization using a WebGIS application. Analysis of landslide database contents shows that in most parts of Germany landslides primarily affect transportation infrastructures. Although with distinct lower frequency, recent landslides are also recorded to cause serious damage to hydraulic facilities and waterways, supply and disposal infrastructures, sites of cultural heritage, as well as forest, agricultural, and mining areas. The main types of landslide damage are failure of cut and fill slopes, destruction of retaining walls, street lights, and forest stocks, burial of roads, backyards, and garden areas, as well as crack formation in foundations, sewer lines, and building walls. Landslide repair and mitigation at transportation infrastructures is dominated by simple solutions such as catch barriers or rock fall drapery. These solutions are often undersized and fail under stress. The use of costly slope stabilization or protection systems is proven to reduce these risks effectively over longer maintenance cycles. The right balancing of landslide mitigation is thus a crucial problem in managing landslide risks. Development and analysis of such landslide databases helps to support decision-makers in finding efficient solutions to minimize landslide risks for human beings, infrastructures, and financial assets.

The Windows to the Universe Project: A Facility for Inter-American Geoscience Education and Outreach

NASA Astrophysics Data System (ADS)

Johnson, R. M.; Lagrave, M.; Araujo-Pradere, E.; Russell, R.; Gardiner, L.; Bergman, J.; Genyuk, J.; Henderson, S.; Dimarco, M.; Metcalfe, T.

2005-05-01

Windows to the Universe (http://www.windows.ucar.edu) is a popular and comprehensive Earth and space science education web site that uses an interdisciplinary approach to engage our global audience. The entire Windows to the Universe site (roughly 7,000 pages) is being translated into Spanish, with support from the National Science Foundation. Large portions have already been "published" to the web and have been in use since October 2003. Web site statistics indicate that use of the Spanish portion of the site has quickly ramped up to ~20% of total site traffic. Approximately 150,000 users per month have accessed the Spanish-language segments of the site over the past academic year, in addition to the visitors to the English version of the website. The largest fraction of non-US users of the Spanish website come from Mexico, with growing use from countries from Central and South America and Spain. A total of 6.7 million users from around the world accessed the educational resources on this comprehensive website in 2004. An exciting new web-based development interface utilizing templates and an image database allows scientists from around the world to collaborate with the Windows to the Universe team, becoming remote developers on the website. This approach has proven to work effectively for scientists eager to efficiently get their science research results out to the public, taking advantage of their specialized expertise and yet not requiring them to become specialists in informal or formal K-12 education.

Design and implementation of a fault-tolerant and dynamic metadata database for clinical trials

NASA Astrophysics Data System (ADS)

Lee, J.; Zhou, Z.; Talini, E.; Documet, J.; Liu, B.

2007-03-01

In recent imaging-based clinical trials, quantitative image analysis (QIA) and computer-aided diagnosis (CAD) methods are increasing in productivity due to higher resolution imaging capabilities. A radiology core doing clinical trials have been analyzing more treatment methods and there is a growing quantity of metadata that need to be stored and managed. These radiology centers are also collaborating with many off-site imaging field sites and need a way to communicate metadata between one another in a secure infrastructure. Our solution is to implement a data storage grid with a fault-tolerant and dynamic metadata database design to unify metadata from different clinical trial experiments and field sites. Although metadata from images follow the DICOM standard, clinical trials also produce metadata specific to regions-of-interest and quantitative image analysis. We have implemented a data access and integration (DAI) server layer where multiple field sites can access multiple metadata databases in the data grid through a single web-based grid service. The centralization of metadata database management simplifies the task of adding new databases into the grid and also decreases the risk of configuration errors seen in peer-to-peer grids. In this paper, we address the design and implementation of a data grid metadata storage that has fault-tolerance and dynamic integration for imaging-based clinical trials.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

PubMed

Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka

2015-11-23

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

The Ensembl genome database project.

PubMed

Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

2002-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

A Data Management Framework for Real-Time Water Quality Monitoring

NASA Astrophysics Data System (ADS)

Mulyono, E.; Yang, D.; Craig, M.

2007-12-01

CSU East Bay operates two in-situ, near-real-time water quality monitoring stations in San Francisco Bay as a member of the Center for Integrative Coastal Ocean Observation, Research, and Education (CICORE) and the Central and Northern California Ocean Observing System (CeNCOOS). We have been operating stations at Dumbarton Pier and San Leandro Marina for the past two years. At each station, a sonde measures seven water quality parameters every six minutes. During the first year of operation, we retrieved data from the sondes every few weeks by visiting the sites and uploading data to a handheld logger. Last year we implemented a telemetry system utilizing a cellular CDMA modem to transfer data from the field to our data center on an hourly basis. Data from each station are initially stored in monthly files in native format. We import data from these files into a SQL database every hour. SQL is handled by Django, an open source web framework. Django provides a user- friendly web user interface (UI) to administer the data. We utilized parts of the Django UI for our database web- front, which allows users to access our database via the World Wide Web and perform basic queries. We also serve our data to other aggregating sites, including the central CICORE website and NOAA's National Data Buoy Center (NDBC). Since Django is written in Python, it allows us to integrate other Python modules into our software, such as the Matplot library for scientific graphics. We store our code in a Subversion repository, which keeps track of software revisions. Code is tested using Python's unittest and doctest modules within Django's testing facility, which warns us when our code modifications cause other parts of the software to break. During the past two years of data acquisition, we have incrementally updated our data model to accommodate changes in physical hardware, including equipment moves, instrument replacements, and sensor upgrades that affected data format.

The HyperLeda project en route to the astronomical virtual observatory

NASA Astrophysics Data System (ADS)

Golev, V.; Georgiev, V.; Prugniel, Ph.

2002-07-01

HyperLeda (Hyper-Linked Extragalactic Databases and Archives) is aimed to study the evolution of galaxies, their kinematics and stellar populations and the structure of Local Universe. HyperLeda is involved in catalogue and software production, data-mining and massive data processing. The products are serviced to the community through web mirrors. The development of HyperLeda is distributed between different sites and is based on the background experience of the LEDA and Hypercat databases. The HyperLeda project is focused both on the European iAstro colaboration and as a unique database for studies of the physics of the extragalactic objects.

Human retroviruses and AIDS 1997

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

Korber, B.; Foley, B.; Leitner, T.

1997-12-01

This compendium is the result of an effort to compile, organize, and rapidly publish as much relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses as possible. The scope of the compendium and database is best summarized by the four parts that it comprises: (1) Nucleic Acid Alignments, (2) Amino Acid Alignments, (3) Reviews and Analyses, and (4) Related Sequences. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. This year we are not including floppy diskettes as the entire compendium is available both at our Web site and at ourmore » ftp site. If you need floppy diskettes please contact either Bette Korber (btk@t10.lanl.gov) or Kersti Rock (karm@t10.lanl.gov) by email or fax ((505) 665-4453). While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. The exception to this are reviews submitted by experts in areas deemed of particular and basic importance to research involving AIDS viral sequence information. These are included in Part III, and are contributed by scientists with particular expertise in the area of interest. In addition to the general descriptions below of the parts of the compendium, the user should read the individual introductions for each part.« less

Readability assessment of internet-based patient education materials related to uterine artery embolization.

PubMed

Shukla, Pratik; Sanghvi, Saurin P; Lelkes, Valdis M; Kumar, Abhishek; Contractor, Sohail

2013-04-01

To determine the readability of Internet-based patient education materials (IPEMs) created by United States hospitals and universities and clinical practices and miscellaneous health care-associated Web sites regarding uterine artery embolization (UAE) as a marker for IPEMs in general. Two hundred unique Web sites were evaluated for patient-related articles on UAE. Web sites produced by US hospitals and universities and clinical practices, as well as miscellaneous health care-associated Web sites meeting the Health on the Net Foundation Code of Conduct criteria were included in the database. By using mathematical regression algorithms based on word and sentence length to quantitatively analyze reading materials for language intricacy, readability of 40 UAE-related IPEMs was assessed with four indices: Flesch-Kincaid Grade Level (FKGL), Flesch Reading Ease Score (FRES), Simple Measure of Gobbledygook (SMOG), and Gunning Frequency of Gobbledygook (GFOG). Scores were evaluated against national recommendations, and intergroup analysis was performed. None of the IPEMs were written at or below the sixth-grade reading level, based on FKGL. The mean readability scores were as follows: FRES, 43.98; FKGL, 10.76; SMOG, 13.63; and GFOG, 14.55. These scores indicate that the readability of UAE IPEMs is written at an advanced level, significantly above the recommended 6th grade reading level (P<.05) determined by the United States Department of Health and Human Services. IPEMs related to UAE generated by hospitals, clinical practices, and miscellaneous health care-associated Web sites are written above the recommended sixth grade level. IPEMs for other disease entities may also reflect similar results. Copyright © 2013 SIR. Published by Elsevier Inc. All rights reserved.

Secure web-based access to radiology: forms and databases for fast queries

NASA Astrophysics Data System (ADS)

McColl, Roderick W.; Lane, Thomas J.

2002-05-01

Currently, Web-based access to mini-PACS or similar databases commonly utilizes either JavaScript, Java applets or ActiveX controls. Many sites do not permit applets or controls or other binary objects for fear of viruses or worms sent by malicious users. In addition, the typical CGI query mechanism requires several parameters to be sent with the http GET/POST request, which may identify the patient in some way; this in unacceptable for privacy protection. Also unacceptable are pages produced by server-side scripts which can be cached by the browser, since these may also contain sensitive information. We propose a simple mechanism for access to patient information, including images, which guarantees security of information, makes it impossible to bookmark the page, or to return to the page after some defined length of time. In addition, this mechanism is simple, therefore permitting rapid access without the need to initially download an interface such as an applet or control. In addition to image display, the design of the site allows the user to view and save movies of multi-phasic data, or to construct multi-frame datasets from entire series. These capabilities make the site attractive for research purposes such as teaching file preparation.

A Distributed Web-based Solution for Ionospheric Model Real-time Management, Monitoring, and Short-term Prediction

NASA Astrophysics Data System (ADS)

Kulchitsky, A.; Maurits, S.; Watkins, B.

2006-12-01

With the widespread availability of the Internet today, many people can monitor various scientific research activities. It is important to accommodate this interest providing on-line access to dynamic and illustrative Web-resources, which could demonstrate different aspects of ongoing research. It is especially important to explain and these research activities for high school and undergraduate students, thereby providing more information for making decisions concerning their future studies. Such Web resources are also important to clarify scientific research for the general public, in order to achieve better awareness of research progress in various fields. Particularly rewarding is dissemination of information about ongoing projects within Universities and research centers to their local communities. The benefits of this type of scientific outreach are mutual, since development of Web-based automatic systems is prerequisite for many research projects targeting real-time monitoring and/or modeling of natural conditions. Continuous operation of such systems provide ongoing research opportunities for the statistically massive validation of the models, as well. We have developed a Web-based system to run the University of Alaska Fairbanks Polar Ionospheric Model in real-time. This model makes use of networking and computational resources at the Arctic Region Supercomputing Center. This system was designed to be portable among various operating systems and computational resources. Its components can be installed across different computers, separating Web servers and computational engines. The core of the system is a Real-Time Management module (RMM) written Python, which facilitates interactions of remote input data transfers, the ionospheric model runs, MySQL database filling, and PHP scripts for the Web-page preparations. The RMM downloads current geophysical inputs as soon as they become available at different on-line depositories. This information is processed to provide inputs for the next ionospheic model time step and then stored in a MySQL database as the first part of the time-specific record. The RMM then performs synchronization of the input times with the current model time, prepares a decision on initialization for the next model time step, and monitors its execution. Then, as soon as the model completes computations for the next time step, RMM visualizes the current model output into various short-term (about 1-2 hours) forecasting products and compares prior results with available ionospheric measurements. The RMM places prepared images into the MySQL database, which can be located on a different computer node, and then proceeds to the next time interval continuing the time-loop. The upper-level interface of this real-time system is the a PHP-based Web site (http://www.arsc.edu/SpaceWeather/new). This site provides general information about the Earth polar and adjacent mid-latitude ionosphere, allows for monitoring of the current developments and short-term forecasts, and facilitates access to the comparisons archive stored in the database.

A Java API for working with PubChem datasets.

PubMed

Southern, Mark R; Griffin, Patrick R

2011-03-01

PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

17 CFR 232.105 - Limitation on use of HTML documents and hypertext links.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Limitation on use of HTML... Requirements § 232.105 Limitation on use of HTML documents and hypertext links. (a) Electronic filers must... EDGAR database on the Commission's public web site (www.sec.gov). Electronic filers also may include...

How Homeland Security Affects Spatial Information

ERIC Educational Resources Information Center

Zellmer, Linda

2004-01-01

A recent article in Security-Focus described the fact that several U.S. government buildings in Washington DC could no longer be clearly seen by people using MapQuest's aerial photo database. In addition, the photos of these buildings were altered at the Web sites wherein they are posted at the request of the U.S. Secret Service. This is an…

Digital Library Services: Perceptions and Expectations of User Communities and Librarians in a New Zealand Academic Library.

ERIC Educational Resources Information Center

Xia, Wei

2003-01-01

Provides an overview of research conducted at Victoria University of Wellington regarding differing perceptions and expectations of user communities and librarians related to the usability of digital services. Considers access to services, currency of information on the Web site, the online public access catalog, databases, electronic journals,…

The North Carolina State University Libraries Search Experience: Usability Testing Tabbed Search Interfaces for Academic Libraries

ERIC Educational Resources Information Center

Teague-Rector, Susan; Ballard, Angela; Pauley, Susan K.

2011-01-01

Creating a learnable, effective, and user-friendly library Web site hinges on providing easy access to search. Designing a search interface for academic libraries can be particularly challenging given the complexity and range of searchable library collections, such as bibliographic databases, electronic journals, and article search silos. Library…

Mind Maps: Hot New Tools Proposed for Cyberspace Librarians.

ERIC Educational Resources Information Center

Humphreys, Nancy K.

1999-01-01

Describes how online searchers can use a software tool based on back-of-the-book indexes to assist in dealing with search engine databases compiled by spiders that crawl across the entire Internet or through large Web sites. Discusses human versus machine knowledge, conversion of indexes to mind maps or mini-thesauri, middleware, eXtensible Markup…

ZINC: A Free Tool to Discover Chemistry for Biology

PubMed Central

2012-01-01

ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org. PMID:22587354

Equipment Management for Sensor Networks: Linking Physical Infrastructure and Actions to Observational Data

NASA Astrophysics Data System (ADS)

Jones, A. S.; Horsburgh, J. S.; Matos, M.; Caraballo, J.

2015-12-01

Networks conducting long term monitoring using in situ sensors need the functionality to track physical equipment as well as deployments, calibrations, and other actions related to site and equipment maintenance. The observational data being generated by sensors are enhanced if direct linkages to equipment details and actions can be made. This type of information is typically recorded in field notebooks or in static files, which are rarely linked to observations in a way that could be used to interpret results. However, the record of field activities is often relevant to analysis or post-processing of the observational data. We have developed an underlying database schema and deployed a web interface for recording and retrieving information on physical infrastructure and related actions for observational networks. The database schema for equipment was designed as an extension to the Observations Data Model 2 (ODM2), a community-developed information model for spatially discrete, feature based earth observations. The core entities of ODM2 describe location, observed variable, and timing of observations, and the equipment extension contains entities to provide additional metadata specific to the inventory of physical infrastructure and associated actions. The schema is implemented in a relational database system for storage and management with an associated web interface. We designed the web-based tools for technicians to enter and query information on the physical equipment and actions such as site visits, equipment deployments, maintenance, and calibrations. These tools were implemented for the iUTAH (innovative Urban Transitions and Aridregion Hydrosustainability) ecohydrologic observatory, and we anticipate that they will be useful for similar large-scale monitoring networks desiring to link observing infrastructure to observational data to increase the quality of sensor-based data products.

Ten years of change: National Library of Medicine TOXMAP gets a new look.

PubMed

Hochstein, Colette; Gemoets, Darren; Goshorn, Jeanne

2014-01-01

The United States National Library of Medicine (NLM) TOXNET® databases < http://toxnet.nlm.nih.gov > provide broad coverage of environmental health information covering a wide variety of topics, including access to the U.S. Environment Protection Agency (EPA)'s Toxics Release Inventory (TRI) data. The NLM web-based geographic information system (GIS), TOXMAP® < http://toxmap.nlm.nih.gov/ >, provides interactive maps which show where TRI chemicals are released into the environment and links to TOXNET for information about these chemicals. TOXMAP also displays locations of Superfund sites on the EPA National Priority List, as well as information about the chemical contaminants at these sites. This column focuses on a new version of TOXMAP which brings it up to date with current web GIS technologies and user expectations.

Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites.

PubMed

Chou, Kuo-Chen; Shen, Hong-Bin

2007-05-01

One of the critical challenges in predicting protein subcellular localization is how to deal with the case of multiple location sites. Unfortunately, so far, no efforts have been made in this regard except for the one focused on the proteins in budding yeast only. For most existing predictors, the multiple-site proteins are either excluded from consideration or assumed even not existing. Actually, proteins may simultaneously exist at, or move between, two or more different subcellular locations. For instance, according to the Swiss-Prot database (version 50.7, released 19-Sept-2006), among the 33,925 eukaryotic protein entries that have experimentally observed subcellular location annotations, 2715 have multiple location sites, meaning about 8% bearing the multiplex feature. Proteins with multiple locations or dynamic feature of this kind are particularly interesting because they may have some very special biological functions intriguing to investigators in both basic research and drug discovery. Meanwhile, according to the same Swiss-Prot database, the number of total eukaryotic protein entries (except those annotated with "fragment" or those with less than 50 amino acids) is 90,909, meaning a gap of (90,909-33,925) = 56,984 entries for which no knowledge is available about their subcellular locations. Although one can use the computational approach to predict the desired information for the blank, so far, all the existing methods for predicting eukaryotic protein subcellular localization are limited in the case of single location site only. To overcome such a barrier, a new ensemble classifier, named Euk-mPLoc, was developed that can be used to deal with the case of multiple location sites as well. Euk-mPLoc is freely accessible to the public as a Web server at http://202.120.37.186/bioinf/euk-multi. Meanwhile, to support the people working in the relevant areas, Euk-mPLoc has been used to identify all eukaryotic protein entries in the Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The large-scale results thus obtained have been deposited at the same Web site via a downloadable file prepared with Microsoft Excel and named "Tab_Euk-mPLoc.xls". Furthermore, to include new entries of eukaryotic proteins and reflect the continuous development of Euk-mPLoc in both the coverage scope and prediction accuracy, we will timely update the downloadable file as well as the predictor, and keep users informed by publishing a short note in the Journal and making an announcement in the Web Page.

REDIdb: the RNA editing database.

PubMed

Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

2007-01-01

The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

Design and Implementation of an Environmental Mercury Database for Northeastern North America

NASA Astrophysics Data System (ADS)

Clair, T. A.; Evers, D.; Smith, T.; Goodale, W.; Bernier, M.

2002-12-01

An important issue faced when attempting to interpret geochemical variability studies across large regions, is the accumulation, access and consistent display of data from a large number of sources. We were given the opportunity to provide a regional assessment of mercury distribution in surface waters, sediments, invertebrates, fish, and birds in a region extending from New York State to the Island of Newfoundland. We received over 20 individual databases from State, Provincial, and Federal governments, as well as university researchers from both Canada and the United States. These databases came in a variety of formats and sizes. Our challenge was to find a way of accumulating and presenting the large amounts of acquired data, in a consistent, easily accessible fashion, which could then be more easily interpreted. Moreover, the database had to be portable and easily distributable to the large number of study participants. We developed a static database structure using a web-based approach which we were then able to mount on a server which was accessible to all project participants. The site also contained all the necessary documentation related to the data, its acquisition, as well as the methods used in its analysis and interpretation. We then copied the complete web site on CDROM's which we then distributed to all project participants, funding agencies, and other interested parties. The CDROM formed a permanent record of the project and was issued ISSN and ISBN numbers so that the information remained accessible to researchers in perpetuity. Here we present an overview of the CDROM and data structures, of the information accumulated over the first year of the study, and initial interpretation of the results.

Energy science and technology database (on the internet). Online data

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

NONE

The Energy Science and Technology Database (EDB) is a multidisciplinary file containing worldwide references to basic and applied scientific and technical research literature. The information is collected for use by government managers, researchers at the national laboratories, and other research efforts sponsored by the U.S. Department of Energy, and the results of this research are transferred to the public. Abstracts are included for records from 1976 to the present. The EDB also contains the Nuclear Science Abstracts which is a comprehensive abstract and index collection to the international nuclear science and technology literature for the period 1948 through 1976. Includedmore » are scientific and technical reports of the U.S. Atomic Energy Commission, U.S. Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Approximately 25% of the records in the file contain abstracts. Nuclear Science Abstracts contains over 900,000 bibliographic records. The entire Energy Science and Technology Database contains over 3 million bibliographic records. This database is now available for searching through the GOV. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.

PubMed

Ambrosini, Giovanna; Groux, Romain; Bucher, Philipp

2018-03-05

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or TF binding site model from a public database. The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively. giovanna.ambrosini@epfl.ch. SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE.

Electronic Biomedical Literature Search for Budding Researcher

PubMed Central

Thakre, Subhash B.; Thakre S, Sushama S.; Thakre, Amol D.

2013-01-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research. PMID:24179937

Electronic biomedical literature search for budding researcher.

PubMed

Thakre, Subhash B; Thakre S, Sushama S; Thakre, Amol D

2013-09-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

Self-reported information needs of anesthesia residency applicants and analysis of applicant-related web sites resources at 131 United States training programs.

PubMed

Chu, Larry F; Young, Chelsea A; Zamora, Abby K; Lowe, Derek; Hoang, Dan B; Pearl, Ronald G; Macario, Alex

2011-02-01

Despite the use of web-based information resources by both anesthesia departments and applicants, little research has been done to assess these resources and determine whether they are meeting applicant needs. Evidence is needed to guide anesthesia informatics research in developing high-quality anesthesia residency program Web sites (ARPWs). We used an anonymous web-based program (SurveyMonkey, Portland, OR) to distribute a survey investigating the information needs and perceived usefulness of ARPWs to all 572 Stanford anesthesia residency program applicants. A quantitative scoring system was then created to assess the quality of ARPWs in meeting the information needs of these applicants. Two researchers independently analyzed all 131 ARPWs in the United States to determine whether the ARPWs met the needs of applicants based on the scoring system. Finally, a qualitative assessment of the overall user experience of ARPWs was developed to account for the subjective elements of the Web site's presentation. Ninety-eight percent of respondents reported having used ARPWs during the application process. Fifty-six percent reported first visiting the Stanford ARPW when deciding whether to apply to Stanford's anesthesia residency program. Multimedia and Web 2.0 technologies were "very" or "most" useful in "learning intangible aspects of a program, like how happy people are" (42% multimedia and Web 2.0 versus 14% text and photos). ARPWs, on average, contained only 46% of the content items identified as important by applicants. The average (SD) quality scores among all ARPWs was 2.06 (0.59) of 4.0 maximum points. The mean overall qualitative score for all 131 ARPWs was 4.97 (1.92) of 10 points. Only 2% of applicants indicated that the majority (75%-100%) of Web sites they visited provided a complete experience. Anesthesia residency applicants rely heavily on ARPWs to research programs, prepare for interviews, and formulate a rank list. Anesthesia departments can improve their ARPWs by including information such as total hours worked and work hours by rotation (missing in 96% and 97% of ARPWs) and providing a valid web address on the Fellowship and Residency Electronic Interactive Database Access System (FREIDA) (missing in 28% of ARPWs).

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

The Degradome database: mammalian proteases and diseases of proteolysis.

PubMed

Quesada, Víctor; Ordóñez, Gonzalo R; Sánchez, Luis M; Puente, Xose S; López-Otín, Carlos

2009-01-01

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes.

The Degradome database: mammalian proteases and diseases of proteolysis

PubMed Central

Quesada, Víctor; Ordóñez, Gonzalo R.; Sánchez, Luis M.; Puente, Xose S.; López-Otín, Carlos

2009-01-01

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes. PMID:18776217

EPA Facility Registry Service (FRS): Facility Interests Dataset - Intranet

EPA Pesticide Factsheets

This web feature service consists of location and facility identification information from EPA's Facility Registry Service (FRS) for all sites that are available in the FRS individual feature layers. The layers comprise the FRS major program databases, including:Assessment Cleanup and Redevelopment Exchange System (ACRES) : brownfields sites ; Air Facility System (AFS) : stationary sources of air pollution ; Air Quality System (AQS) : ambient air pollution data from monitoring stations; Bureau of Indian Affairs (BIA) : schools data on Indian land; Base Realignment and Closure (BRAC) facilities; Clean Air Markets Division Business System (CAMDBS) : market-based air pollution control programs; Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) : hazardous waste sites; Integrated Compliance Information System (ICIS) : integrated enforcement and compliance information; National Compliance Database (NCDB) : Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Toxic Substances Control Act (TSCA); National Pollutant Discharge Elimination System (NPDES) module of ICIS : NPDES surface water permits; Radiation Information Database (RADINFO) : radiation and radioactivity facilities; RACT/BACT/LAER Clearinghouse (RBLC) : best available air pollution technology requirements; Resource Conservation and Recovery Act Information System (RCRAInfo) : tracks generators, transporters, treaters, storers, and disposers of haz

EPA Facility Registry Service (FRS): Facility Interests Dataset

EPA Pesticide Factsheets

This web feature service consists of location and facility identification information from EPA's Facility Registry Service (FRS) for all sites that are available in the FRS individual feature layers. The layers comprise the FRS major program databases, including:Assessment Cleanup and Redevelopment Exchange System (ACRES) : brownfields sites ; Air Facility System (AFS) : stationary sources of air pollution ; Air Quality System (AQS) : ambient air pollution data from monitoring stations; Bureau of Indian Affairs (BIA) : schools data on Indian land; Base Realignment and Closure (BRAC) facilities; Clean Air Markets Division Business System (CAMDBS) : market-based air pollution control programs; Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) : hazardous waste sites; Integrated Compliance Information System (ICIS) : integrated enforcement and compliance information; National Compliance Database (NCDB) : Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Toxic Substances Control Act (TSCA); National Pollutant Discharge Elimination System (NPDES) module of ICIS : NPDES surface water permits; Radiation Information Database (RADINFO) : radiation and radioactivity facilities; RACT/BACT/LAER Clearinghouse (RBLC) : best available air pollution technology requirements; Resource Conservation and Recovery Act Information System (RCRAInfo) : tracks generators, transporters, treaters, storers, and disposers of haz

Androgen-responsive gene database: integrated knowledge on androgen-responsive genes.

PubMed

Jiang, Mei; Ma, Yunsheng; Chen, Congcong; Fu, Xuping; Yang, Shu; Li, Xia; Yu, Guohua; Mao, Yumin; Xie, Yi; Li, Yao

2009-11-01

Androgen signaling plays an important role in many biological processes. Androgen Responsive Gene Database (ARGDB) is devoted to providing integrated knowledge on androgen-controlled genes. Gene records were collected on the basis of PubMed literature collections. More than 6000 abstracts and 950 original publications were manually screened, leading to 1785 human genes, 993 mouse genes, and 583 rat genes finally included in the database. All the collected genes were experimentally proved to be regulated by androgen at the expression level or to contain androgen-responsive regions. For each gene important details of the androgen regulation experiments were collected from references, such as expression change, androgen-responsive sequence, response time, tissue/cell type, experimental method, ligand identity, and androgen amount, which will facilitate further evaluation by researchers. Furthermore, the database was integrated with multiple annotation resources, including National Center for Biotechnology Information, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway, to reveal the biological characteristics and significance of androgen-regulated genes. The ARGDB web site is mainly composed of the Browse, Search, Element Scan, and Submission modules. It is user friendly and freely accessible at http://argdb.fudan.edu.cn. Preliminary analysis of the collected data was performed. Many disease pathways, such as prostate carcinogenesis, were found to be enriched in androgen-regulated genes. The discovered androgen-response motifs were similar to those in previous reports. The analysis results are displayed in the web site. In conclusion, ARGDB provides a unified gateway to storage, retrieval, and update of information on androgen-regulated genes.

Business Faculty Research: Satisfaction with the Web versus Library Databases

ERIC Educational Resources Information Center

Dewald, Nancy H.; Silvius, Matthew A.

2005-01-01

Business faculty members teaching at undergraduate campuses of the Pennsylvania State University were surveyed in order to assess their satisfaction with free Web sources and with subscription databases for their professional research. Although satisfaction with the Web's ease of use was higher than that for databases, overall satisfaction for…

A Web-Based Database for Nurse Led Outreach Teams (NLOT) in Toronto.

PubMed

Li, Shirley; Kuo, Mu-Hsing; Ryan, David

2016-01-01

A web-based system can provide access to real-time data and information. Healthcare is moving towards digitizing patients' medical information and securely exchanging it through web-based systems. In one of Ontario's health regions, Nurse Led Outreach Teams (NLOT) provide emergency mobile nursing services to help reduce unnecessary transfers from long-term care homes to emergency departments. Currently the NLOT team uses a Microsoft Access database to keep track of the health information on the residents that they serve. The Access database lacks scalability, portability, and interoperability. The objective of this study is the development of a web-based database using Oracle Application Express that is easily accessible from mobile devices. The web-based database will allow NLOT nurses to enter and access resident information anytime and from anywhere.

The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource

PubMed Central

2012-01-01

Background Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species. Description The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers (“Isolate Accession”), the first five of which correspond to the collection site (“Environmental Accession”). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages. Conclusions HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/. PMID:23095476

DPS Planetary Science Graduate Programs Database for Students and Advisors

NASA Astrophysics Data System (ADS)

Klassen, David R.; Roman, Anthony; Meinke, Bonnie K.

2016-10-01

Several years ago the DPS Education committee decided that it should have an online resource that could help undergraduate students find graduate programs that could lead to a PhD with a focus in planetary science. It began in 2013 as a static page of information and evolved from there to a database-driven web site. Visitors can browse the entire list of programs or create a subset listing based on several filters. The site should be of use not only to undergraduates looking for programs, but also for advisers looking to help their students decide on their future plans. The reason for such a list is that "planetary science" is a heading that covers an extremely diverse set of disciplines. The usual case is that planetary scientists are housed in a discipline-placed department so that finding them is typically not easy—undergraduates cannot look for a Planetary Science department, but must (somehow) know to search for them in all their possible places. This can overwhelm even determined undergraduate student, and even many advisers!We present here the updated site and a walk-through of the basic features as well as some usage statistics from the collected web site analytics. We ask for community feedback on additional features to make the system more usable for them. We also call upon those mentoring and advising undergraduates to use this resource, and for program admission chairs to continue to review their entry and provide us with the most up-to-date information.The URL for our site is http://dps.aas.org/education/graduate-schools.

ProMateus—an open research approach to protein-binding sites analysis

PubMed Central

Neuvirth, Hani; Heinemann, Uri; Birnbaum, David; Tishby, Naftali; Schreiber, Gideon

2007-01-01

The development of bioinformatic tools by individual labs results in the abundance of parallel programs for the same task. For example, identification of binding site regions between interacting proteins is done using: ProMate, WHISCY, PPI-Pred, PINUP and others. All servers first identify unique properties of binding sites and then incorporate them into a predictor. Obviously, the resulting prediction would improve if the most suitable parameters from each of those predictors would be incorporated into one server. However, because of the variation in methods and databases, this is currently not feasible. Here, the protein-binding site prediction server is extended into a general protein-binding sites research tool, ProMateus. This web tool, based on ProMate's infrastructure enables the easy exploration and incorporation of new features and databases by the user, providing an evaluation of the benefit of individual features and their combination within a set framework. This transforms the individual research into a community exercise, bringing out the best from all users for optimized predictions. The analysis is demonstrated on a database of protein protein and protein-DNA interactions. This approach is basically different from that used in generating meta-servers. The implications of the open-research approach are discussed. ProMateus is available at http://bip.weizmann.ac.il/promate. PMID:17488838

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

The ASTARTE Paleotsunami Deposits data base - web-based references for tsunami research in the NEAM region

NASA Astrophysics Data System (ADS)

De Martini, P. M.; Pantosti, D.; Orefice, S.; Smedile, A.; Patera, A.; Paris, R.; Terrinha, P.; Hunt, J.; Papadopoulos, G. A.; Noiva, J.; Triantafyllou, I.; Yalciner, A. C.

2017-12-01

EU project ASTARTE aimed at developing a higher level of tsunami hazard assessment in the North-Eastern Atlantic, the Mediterranean and connected seas (NEAM) region by a combination of field work, experimental work, numerical modeling and technical development. The project was a cooperative work of 26 institutes from 16 countries and linked together the description of past tsunamigenic events, the identification and characterization of tsunami sources, the calculation of the impact of such events, and the development of adequate resilience and risks mitigation strategies (http://www.astarte-project.eu/). Within ASTARTE, a web-based database on Paleotsunami Deposits in the NEAM area was created with the purpose to be the future information repository for tsunami research in the broad region. The aim of the project is the integration of every existing official scientific reports and peer reviewed papers on this topic. The database, which archives information and detailed data crucial for tsunami modeling, will be updated on new entries every 12 months. A relational database managed by ArcGIS for Desktop 10.x software has been implemented. One of the final goals of the project is the public sharing of the archived dataset through a web-based map service that will allow visualizing, querying, analyzing, and interpreting the dataset. The interactive map service is hosted by ArcGIS Online and will deploy the cloud capabilities of the portal. Any interested users will be able to access the online GIS resources through any Internet browser or specific apps that run on desktop machines, smartphones, or tablets and will be able to use the analytical tools, key tasks, and workflows of the service. We will present the database structure (characterized by the presence of two main tables: the Site table and the Event table) and topics as well as their ArcGIS Online version. To date, a total of 151 sites and 220 tsunami evidence have been recorded within the ASTARTE database. The ASTARTE Paleotsunami Deposits database - NEAM region is now available online at the address http://arcg.is/1CWz0. The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 603839 (Project ASTARTE - Assessment, Strategy and Risk Reduction for Tsunamis in Europe).

76 FR 40497 - Medicare Program; Changes to the End-Stage Renal Disease Prospective Payment System for CY 2012...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-08

...] RIN 0938-AQ27 Medicare Program; Changes to the End-Stage Renal Disease Prospective Payment System for... through Federal Digital System (FDsys), a service of the U.S. Government Printing Office. This database... Internet on the CMS Web site. The Addenda to the End-Stage Renal Disease (ESRD) Prospective Payment System...

An Ounce of Prevention: Technologists Use Network-Access Control to Protect System Resources, Students

ERIC Educational Resources Information Center

Bolch, Matt

2009-01-01

Whether for an entire district, a single campus, or one classroom, allowing authorized access to a computer network can be fraught with challenges. The login process should be fairly seamless to approved users, giving them speedy access to approved Web sites, databases, and other sources of information. It also should be tough on unauthorized…

Discrepancy Reporting Management System

NASA Technical Reports Server (NTRS)

Cooper, Tonja M.; Lin, James C.; Chatillon, Mark L.

2004-01-01

Discrepancy Reporting Management System (DRMS) is a computer program designed for use in the stations of NASA's Deep Space Network (DSN) to help establish the operational history of equipment items; acquire data on the quality of service provided to DSN customers; enable measurement of service performance; provide early insight into the need to improve processes, procedures, and interfaces; and enable the tracing of a data outage to a change in software or hardware. DRMS is a Web-based software system designed to include a distributed database and replication feature to achieve location-specific autonomy while maintaining a consistent high quality of data. DRMS incorporates commercial Web and database software. DRMS collects, processes, replicates, communicates, and manages information on spacecraft data discrepancies, equipment resets, and physical equipment status, and maintains an internal station log. All discrepancy reports (DRs), Master discrepancy reports (MDRs), and Reset data are replicated to a master server at NASA's Jet Propulsion Laboratory; Master DR data are replicated to all the DSN sites; and Station Logs are internal to each of the DSN sites and are not replicated. Data are validated according to several logical mathematical criteria. Queries can be performed on any combination of data.

PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.

PubMed

García-Remesal, Miguel; Cuevas, Alejandro; Pérez-Rey, David; Martín, Luis; Anguita, Alberto; de la Iglesia, Diana; de la Calle, Guillermo; Crespo, José; Maojo, Víctor

2010-11-01

PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching for papers mentioning one or more specific sequences of nucleic acids and (ii) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that we created by using the full text of the 176 672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically extract the genetic sequences occurring in each paper, we used an original method we have developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index new manuscripts. Users can query the database via the web interface provided. PubDNA Finder can be freely accessed at http://servet.dia.fi.upm.es:8080/pubdnafinder

Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

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

Myers, G.; Foley, B.; Korber, B.

1997-04-01

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived.more » Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.« less

BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska.

NASA Astrophysics Data System (ADS)

Cody, R. P.; Kassin, A.; Kofoed, K. B.; Copenhaver, W.; Laney, C. M.; Gaylord, A. G.; Collins, J. A.; Tweedie, C. E.

2014-12-01

The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic and the Barrow Area Information Database (BAID, www.barrowmapped.org) tracks and facilitates a gamut of research, management, and educational activities in the area. BAID is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 12,000 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, save or print maps and query results, and filter or view information by space, time, and/or other tags. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. Recent advances include the addition of more than 2000 new research sites, provision of differential global position system (dGPS) and Unmanned Aerial Vehicle (UAV) support to visiting scientists, surveying over 80 miles of coastline to document rates of erosion, training of local GIS personal to better make use of science in local decision making, deployment and near real time connectivity to a wireless micrometeorological sensor network, links to Barrow area datasets housed at national data archives and substantial upgrades to the BAID website and web mapping applications.

Facilitating Collaboration, Knowledge Construction and Communication with Web-Enabled Databases.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of World Wide Web-enabled databases that dynamically generate Web materials and focuses on the use of this technology to support collaboration, knowledge construction, and communication. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and…

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

Cancer registries in Japan: National Clinical Database and site-specific cancer registries.

PubMed

Anazawa, Takayuki; Miyata, Hiroaki; Gotoh, Mitsukazu

2015-02-01

The cancer registry is an essential part of any rational program of evidence-based cancer control. The cancer control program is required to strategize in a systematic and impartial manner and efficiently utilize limited resources. In Japan, the National Clinical Database (NCD) was launched in 2010. It is a nationwide prospective registry linked to various types of board certification systems regarding surgery. The NCD is a nationally validated database using web-based data collection software; it is risk adjusted and outcome based to improve the quality of surgical care. The NCD generalizes site-specific cancer registries by taking advantage of their excellent organizing ability. Some site-specific cancer registries, including pancreatic, breast, and liver cancer registries have already been combined with the NCD. Cooperation between the NCD and site-specific cancer registries can establish a valuable platform to develop a cancer care plan in Japan. Furthermore, the prognosis information of cancer patients arranged using population-based and hospital-based cancer registries can help in efficient data accumulation on the NCD. International collaboration between Japan and the USA has recently started and is expected to provide global benchmarking and to allow a valuable comparison of cancer treatment practices between countries using nationwide cancer registries in the future. Clinical research and evidence-based policy recommendation based on accurate data from the nationwide database may positively impact the public.

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

PubMed

Ito, Jun-ichi; Ikeda, Kazuyoshi; Yamada, Kazunori; Mizuguchi, Kenji; Tomii, Kentaro

2015-01-01

PoSSuM (http://possum.cbrc.jp/PoSSuM/) is a database for detecting similar small-molecule binding sites on proteins. Since its initial release in 2011, PoSSuM has grown to provide information related to 49 million pairs of similar binding sites discovered among 5.5 million known and putative binding sites. This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery. In this release, we have provided a new service named PoSSuM drug search (PoSSuMds) at http://possum.cbrc.jp/PoSSuM/drug_search/, in which we selected 194 approved drug compounds retrieved from ChEMBL, and detected their known binding pockets and pockets that are similar to them. Users can access and download all of the search results via a new web interface, which is useful for finding ligand analogs as well as potential target proteins. Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM. Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Java API for working with PubChem datasets

PubMed Central

Southern, Mark R.; Griffin, Patrick R.

2011-01-01

Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability: http://code.google.com/p/pubchemdb Contact: southern@scripps.edu PMID:21216779

sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank.

PubMed

Kellenberger, Esther; Muller, Pascal; Schalon, Claire; Bret, Guillaume; Foata, Nicolas; Rognan, Didier

2006-01-01

The sc-PDB is a collection of 6 415 three-dimensional structures of binding sites found in the Protein Data Bank (PDB). Binding sites were extracted from all high-resolution crystal structures in which a complex between a protein cavity and a small-molecular-weight ligand could be identified. Importantly, ligands are considered from a pharmacological and not a structural point of view. Therefore, solvents, detergents, and most metal ions are not stored in the sc-PDB. Ligands are classified into four main categories: nucleotides (< 4-mer), peptides (< 9-mer), cofactors, and organic compounds. The corresponding binding site is formed by all protein residues (including amino acids, cofactors, and important metal ions) with at least one atom within 6.5 angstroms of any ligand atom. The database was carefully annotated by browsing several protein databases (PDB, UniProt, and GO) and storing, for every sc-PDB entry, the following features: protein name, function, source, domain and mutations, ligand name, and structure. The repository of ligands has also been archived by diversity analysis of molecular scaffolds, and several chemoinformatics descriptors were computed to better understand the chemical space covered by stored ligands. The sc-PDB may be used for several purposes: (i) screening a collection of binding sites for predicting the most likely target(s) of any ligand, (ii) analyzing the molecular similarity between different cavities, and (iii) deriving rules that describe the relationship between ligand pharmacophoric points and active-site properties. The database is periodically updated and accessible on the web at http://bioinfo-pharma.u-strasbg.fr/scPDB/.

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

PubMed

Mazzarelli, Joan M; Brestelli, John; Gorski, Regina K; Liu, Junmin; Manduchi, Elisabetta; Pinney, Deborah F; Schug, Jonathan; White, Peter; Kaestner, Klaus H; Stoeckert, Christian J

2007-01-01

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

PubMed

Nadkarni, P M; Brandt, C M; Marenco, L

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

CMO: Cruise Metadata Organizer for JAMSTEC Research Cruises

NASA Astrophysics Data System (ADS)

Fukuda, K.; Saito, H.; Hanafusa, Y.; Vanroosebeke, A.; Kitayama, T.

2011-12-01

JAMSTEC's Data Research Center for Marine-Earth Sciences manages and distributes a wide variety of observational data and samples obtained from JAMSTEC research vessels and deep sea submersibles. Generally, metadata are essential to identify data and samples were obtained. In JAMSTEC, cruise metadata include cruise information such as cruise ID, name of vessel, research theme, and diving information such as dive number, name of submersible and position of diving point. They are submitted by chief scientists of research cruises in the Microsoft Excel° spreadsheet format, and registered into a data management database to confirm receipt of observational data files, cruise summaries, and cruise reports. The cruise metadata are also published via "JAMSTEC Data Site for Research Cruises" within two months after end of cruise. Furthermore, these metadata are distributed with observational data, images and samples via several data and sample distribution websites after a publication moratorium period. However, there are two operational issues in the metadata publishing process. One is that duplication efforts and asynchronous metadata across multiple distribution websites due to manual metadata entry into individual websites by administrators. The other is that differential data types or representation of metadata in each website. To solve those problems, we have developed a cruise metadata organizer (CMO) which allows cruise metadata to be connected from the data management database to several distribution websites. CMO is comprised of three components: an Extensible Markup Language (XML) database, an Enterprise Application Integration (EAI) software, and a web-based interface. The XML database is used because of its flexibility for any change of metadata. Daily differential uptake of metadata from the data management database to the XML database is automatically processed via the EAI software. Some metadata are entered into the XML database using the web-based interface by a metadata editor in CMO as needed. Then daily differential uptake of metadata from the XML database to databases in several distribution websites is automatically processed using a convertor defined by the EAI software. Currently, CMO is available for three distribution websites: "Deep Sea Floor Rock Sample Database GANSEKI", "Marine Biological Sample Database", and "JAMSTEC E-library of Deep-sea Images". CMO is planned to provide "JAMSTEC Data Site for Research Cruises" with metadata in the future.

Databases on biotechnology and biosafety of GMOs.

PubMed

Degrassi, Giuliano; Alexandrova, Nevena; Ripandelli, Decio

2003-01-01

Due to the involvement of scientific, industrial, commercial and public sectors of society, the complexity of the issues concerning the safety of genetically modified organisms (GMOs) for the environment, agriculture, and human and animal health calls for a wide coverage of information. Accordingly, development of the field of biotechnology, along with concerns related to the fate of released GMOs, has led to a rapid development of tools for disseminating such information. As a result, there is a growing number of databases aimed at collecting and storing information related to GMOs. Most of the sites deal with information on environmental releases, field trials, transgenes and related sequences, regulations and legislation, risk assessment documents, and literature. Databases are mainly established and managed by scientific, national or international authorities, and are addressed towards scientists, government officials, policy makers, consumers, farmers, environmental groups and civil society representatives. This complexity can lead to an overlapping of information. The purpose of the present review is to analyse the relevant databases currently available on the web, providing comments on their vastly different information and on the structure of the sites pertaining to different users. A preliminary overview on the development of these sites during the last decade, at both the national and international level, is also provided.

The development of digital library system for drug research information.

PubMed

Kim, H J; Kim, S R; Yoo, D S; Lee, S H; Suh, O K; Cho, J H; Shin, H T; Yoon, J P

1998-01-01

The sophistication of computer technology and information transmission on internet has made various cyber information repository available to information consumers. In the era of information super-highway, the digital library which can be accessed from remote sites at any time is considered the prototype of information repository. Using object-oriented DBMS, the very first model of digital library for pharmaceutical researchers and related professionals in Korea has been developed. The published research papers and researchers' personal information was included in the database. For database with research papers, 13 domestic journals were abstracted and scanned for full-text image files which can be viewed by Internet web browsers. The database with researchers' personal information was also developed and interlinked to the database with research papers. These database will be continuously updated and will be combined with world-wide information as the unique digital library in the field of pharmacy.

Emerging Trends

DTIC Science & Technology

2013-08-08

theft in the CERT Insider Threat Database were associated with foreign social network connections. 1 Verizon. “The 2013 Data Breach Investigations...passwords, opening infected attachments or web sites, etc. 1 Verizon. “The 2013 Data Breach Investigations Report.” http...were experienced by 38% of respondents1 •  The 2013 Verizon Data Breach Report2 reveals •  29% of breaches studied leveraged social tactics •  A

News from Online: What's New with Chime?

NASA Astrophysics Data System (ADS)

Dorland, Liz

2002-07-01

The Chime plugin (pronounced like the bells) provides a simple route to presenting interactive molecular structures to students via the Internet or in classroom presentations. Small inorganic molecules, ionic structures, organic molecules and giant macromolecules can all be viewed in several formats including ball and stick and spacefilling. Extensive Chime resources on the Internet allow chemistry and biochemistry instructors to create their own Web pages or to use some of the many tutorials for students already online. This article describes about twenty Chime-based Web sites in three categories: Chime Resources, Materials for Student and Classroom Use, and Structure Databases. A list of links is provided.

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

High Temperature Superconducting Materials Database

National Institute of Standards and Technology Data Gateway

SRD 62 NIST High Temperature Superconducting Materials Database (Web, free access)   The NIST High Temperature Superconducting Materials Database (WebHTS) provides evaluated thermal, mechanical, and superconducting property data for oxides and other nonconventional superconductors.

Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server.

PubMed

Vohradsky, Jiri; Janda, Ivan; Grünenfelder, Björn; Berndt, Peter; Röder, Daniel; Langen, Hanno; Weiser, Jaroslav; Jenal, Urs

2003-10-01

Here we present the Swiss-Czech Proteomics Server (SWICZ), which hosts the proteomic database summarizing information about the cell cycle of the aquatic bacterium Caulobacter crescentus. The database provides a searchable tool for easy access of global protein synthesis and protein stability data as examined during the C. crescentus cell cycle. Protein synthesis data collected from five different cell cycle stages were determined for each protein spot as a relative value of the total amount of [(35)S]methionine incorporation. Protein stability of pulse-labeled extracts were measured during a chase period equivalent to one cell cycle unit. Quantitative information for individual proteins together with descriptive data such as protein identities, apparent molecular masses and isoelectric points, were combined with information on protein function, genomic context, and the cell cycle stage, and were then assembled in a relational database with a world wide web interface (http://proteom.biomed.cas.cz), which allows the database records to be searched and displays the recovered information. A total of 1250 protein spots were reproducibly detected on two-dimensional gel electropherograms, 295 of which were identified by mass spectroscopy. The database is accessible either through clickable two-dimensional gel electrophoretic maps or by means of a set of dedicated search engines. Basic characterization of the experimental procedures, data processing, and a comprehensive description of the web site are presented. In its current state, the SWICZ proteome database provides a platform for the incorporation of new data emerging from extended functional studies on the C. crescentus proteome.

Nuclear science abstracts (NSA) database 1948--1974 (on the Internet)

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

NONE

Nuclear Science Abstracts (NSA) is a comprehensive abstract and index collection of the International Nuclear Science and Technology literature for the period 1948 through 1976. Included are scientific and technical reports of the US Atomic Energy Commission, US Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Coverage of the literature since 1976 is provided by Energy Science and Technology Database. Approximately 25% of the records in the file contain abstracts. These are from the following volumes of the print Nuclear Science Abstracts: Volumes 12--18, Volume 29, and Volume 33. The database containsmore » over 900,000 bibliographic records. All aspects of nuclear science and technology are covered, including: Biomedical Sciences; Metals, Ceramics, and Other Materials; Chemistry; Nuclear Materials and Waste Management; Environmental and Earth Sciences; Particle Accelerators; Engineering; Physics; Fusion Energy; Radiation Effects; Instrumentation; Reactor Technology; Isotope and Radiation Source Technology. The database includes all records contained in Volume 1 (1948) through Volume 33 (1976) of the printed version of Nuclear Science Abstracts (NSA). This worldwide coverage includes books, conference proceedings, papers, patents, dissertations, engineering drawings, and journal literature. This database is now available for searching through the GOV. Research Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

What Do They Tell Their Students? Business Faculty Acceptance of the Web and Library Databases for Student Research

ERIC Educational Resources Information Center

Dewald, Nancy H.

2005-01-01

Business faculty were surveyed as to their use of free Web resources and subscription databases for their own and their students' research. A much higher percentage of respondents either require or encourage Web use by their students than require or encourage database use, though most also advise use of multiple sources.

Benefits of a comprehensive quality program for cryopreserved PBMC covering 28 clinical trials sites utilizing an integrated, analytical web-based portal

PubMed Central

Ducar, Constance; Smith, Donna; Pinzon, Cris; Stirewalt, Michael; Cooper, Cristine; McElrath, M. Juliana; Hural, John

2014-01-01

The HIV Vaccine Trials Network (HVTN) is a global network of 28 clinical trial sites dedicated to identifying an effective HIV vaccine. Cryopreservation of high-quality peripheral blood mononuclear cells (PBMC) is critical for the assessment of vaccine-induced cellular immune functions. The HVTN PBMC Quality Management Program is designed to ensure viable PBMC are processed, stored and shipped for clinical trial assays from all HVTN clinical trial sites. The program has evolved by developing and incorporating best practices for laboratory and specimen quality and implementing automated, web-based tools. These tools allow the site-affiliated processing laboratories and the central Laboratory Operations Unit to rapidly collect, analyze and report PBMC quality data. The HVTN PBMC Quality Management Program includes five key components: 1) Laboratory Assessment, 2) PBMC Training and Certification, 3) Internal Quality Control, 4) External Quality Control (EQC), and 5) Assay Specimen Quality Control. Fresh PBMC processing data is uploaded from each clinical site processing laboratory to a central HVTN Statistical and Data Management Center database for access and analysis on a web portal. Samples are thawed at a central laboratory for assay or specimen quality control and sample quality data is uploaded directly to the database by the central laboratory. Four year cumulative data covering 23,477 blood draws reveals an average fresh PBMC yield of 1.45×106 ±0.48 cells per milliliter of useable whole blood. 95% of samples were within the acceptable range for fresh cell yield of 0.8–3.2×106 cells/ml of usable blood. Prior to full implementation of the HVTN PBMC Quality Management Program, the 2007 EQC evaluations from 10 international sites showed a mean day 2 thawed viability of 83.1% and recovery of 67.5%. Since then, four year cumulative data covering 3338 specimens used in immunologic assays shows that 99.88% had acceptable viabilities (>66%) for use in cellular assays (mean, 91.46% ±4.5%), and 96.2% had acceptable recoveries (50%–130%) with a mean of recovery of 85.8% ±19.12% of the originally cryopreserved cells. EQC testing revealed that since August 2009, failed recoveries dropped from 4.1% to 1.6% and failed viabilities dropped from 1.0% to 0.3%. The HVTN PBMC quality program provides for laboratory assessment, training and tools for identifying problems, implementing corrective action and monitoring for improvements. These data support the benefits of implementing a comprehensive, web-based PBMC quality program for large clinical trials networks. PMID:24709391

Characterizing Aerosols over Southeast Asia using the AERONET Data Synergy Tool

NASA Technical Reports Server (NTRS)

Giles, David M.; Holben, Brent N.; Eck, Thomas F.; Slutsker, Ilya; Slutsker, Ilya; Welton, Ellsworth, J.; Chin, Mian; Kucsera, Thomas; Schmaltz, Jeffery E.; Diehl, Thomas;

The Giardia genome project database.

PubMed

McArthur, A G; Morrison, H G; Nixon, J E; Passamaneck, N Q; Kim, U; Hinkle, G; Crocker, M K; Holder, M E; Farr, R; Reich, C I; Olsen, G E; Aley, S B; Adam, R D; Gillin, F D; Sogin, M L

2000-08-15

The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.

Structural Ceramics Database

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

The Use of Technology in Participant Tracking and Study Retention: Lessons Learned From a Clinical Trials Network Study.

PubMed

Mitchell, Shannon Gwin; Schwartz, Robert P; Alvanzo, Anika A H; Weisman, Monique S; Kyle, Tiffany L; Turrigiano, Eva M; Gibson, Martha L; Perez, Livangelie; McClure, Erin A; Clingerman, Sara; Froias, Autumn; Shandera, Danielle R; Walker, Robrina; Babcock, Dean L; Bailey, Genie L; Miele, Gloria M; Kunkel, Lynn E; Norton, Michael; Stitzer, Maxine L

2015-01-01

The growing use of newer communication and Internet technologies, even among low-income and transient populations, require research staff to update their outreach strategies to ensure high follow-up and participant retention rates. This paper presents the views of research assistants on the use of cell phones and the Internet to track participants in a multisite randomized trial of substance use disorder treatment. Preinterview questionnaires exploring tracking and other study-related activities were collected from 21 research staff across the 10 participating US sites. Data were then used to construct a semistructured interview guide that, in turn, was used to interview 12 of the same staff members. The questionnaires and interview data were entered in Atlas.ti and analyzed for emergent themes related to the use of technology for participant-tracking purposes. Study staff reported that most participants had cell phones, despite having unstable physical addresses and landlines. The incoming call feature of most cell phones was useful for participants and research staff alike, and texting proved to have additional benefits. However, reliance on participants' cell phones also proved problematic. Even homeless participants were found to have access to the Internet through public libraries and could respond to study staff e-mails. Some study sites opened generic social media accounts, through which study staff sent private messages to participants. However, the institutional review board (IRB) approval process for tracking participants using social media at some sites was prohibitively lengthy. Internet searches through Google, national paid databases, obituaries, and judiciary Web sites were also helpful tools. Research staff perceive that cell phones, Internet searches, and social networking sites were effective tools to achieve high follow-up rates in drug abuse research. Studies should incorporate cell phone, texting, and social network Web site information on locator forms; obtain IRB approval for contacting participants using social networking Web sites; and include Web searches, texting, and the use of social media in staff training as standard operating procedures.

Supplement to the Carcinogenic Potency Database (CPDB): Results ofanimal bioassays published in the general literature through 1997 and bythe National Toxicology Program in 1997-1998

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

Gold, Lois Swirsky; Manley, Neela B.; Slone, Thomas H.

2005-04-08

The Carcinogenic Potency Database (CPDB) is a systematic and unifying resource that standardizes the results of chronic, long-term animal cancer tests which have been conducted since the 1950s. The analyses include sufficient information on each experiment to permit research into many areas of carcinogenesis. Both qualitative and quantitative information is reported on positive and negative experiments that meet a set of inclusion criteria. A measure of carcinogenic potency, TD50 (daily dose rate in mg/kg body weight/day to induce tumors in half of test animals that would have remained tumor-free at zero dose), is estimated for each tissue-tumor combination reported. Thismore » article is the ninth publication of a chronological plot of the CPDB; it presents results on 560 experiments of 188 chemicals in mice, rats, and hamsters from 185 publications in the general literature updated through 1997, and from 15 Reports of the National Toxicology Program in 1997-1998. The test agents cover a wide variety of uses and chemical classes. The CPDB Web Site(http://potency.berkeley.edu/) presents the combined database of all published plots in a variety of formats as well as summary tables by chemical and by target organ, supplemental materials on dosing and survival, a detailed guide to using the plot formats, and documentation of methods and publications. The overall CPDB, including the results in this article, presents easily accessible results of 6153 experiments on 1485 chemicals from 1426 papers and 429 NCI/NTP (National Cancer Institute/National Toxicology program) Technical Reports. A tab-separated format of the full CPDB for reading the data into spreadsheets or database applications is available on the Web Site.« less

Italian Present-day Stress Indicators: IPSI Database

NASA Astrophysics Data System (ADS)

Mariucci, M. T.; Montone, P.

2017-12-01

In Italy, since the 90s of the last century, researches concerning the contemporary stress field have been developing at Istituto Nazionale di Geofisica e Vulcanologia (INGV) with local and regional scale studies. Throughout the years many data have been analysed and collected: now they are organized and available for an easy end-use online. IPSI (Italian Present-day Stress Indicators) database, is the first geo-referenced repository of information on the crustal present-day stress field maintained at INGV through a web application database and website development by Gabriele Tarabusi. Data consist of horizontal stress orientations analysed and compiled in a standardized format and quality-ranked for reliability and comparability on a global scale with other database. Our first database release includes 855 data records updated to December 2015. Here we present an updated version that will be released in 2018, after new earthquake data entry up to December 2017. The IPSI web site (http://ipsi.rm.ingv.it/) allows accessing data on a standard map viewer and choose which data (category and/or quality) to plot easily. The main information of each single element (type, quality, orientation) can be viewed simply going over the related symbol, all the information appear by clicking the element. At the same time, simple basic information on the different data type, tectonic regime assignment, quality ranking method are available with pop-up windows. Data records can be downloaded in some common formats, moreover it is possible to download a file directly usable with SHINE, a web based application to interpolate stress orientations (http://shine.rm.ingv.it). IPSI is mainly conceived for those interested in studying the characters of Italian peninsula and surroundings although Italian data are part of the World Stress Map (http://www.world-stress-map.org/) as evidenced by many links that redirect to this database for more details on standard practices in this field.

EPA Facility Registry Service (FRS): ICIS

EPA Pesticide Factsheets

This web feature service contains location and facility identification information from EPA's Facility Registry Service (FRS) for the subset of facilities that link to the Integrated Compliance Information System (ICIS). When complete, ICIS will provide a database that will contain integrated enforcement and compliance information across most of EPA's programs. The vision for ICIS is to replace EPA's independent databases that contain enforcement data with a single repository for that information. Currently, ICIS contains all Federal Administrative and Judicial enforcement actions and a subset of the Permit Compliance System (PCS), which supports the National Pollutant Discharge Elimination System (NPDES). ICIS exchanges non-sensitive enforcement/compliance activities, non-sensitive formal enforcement actions and NPDES information with FRS. This web feature service contains the enforcement/compliance activities and formal enforcement action related facilities; the NPDES facilities are contained in the PCS_NPDES web feature service. FRS identifies and geospatially locates facilities, sites or places subject to environmental regulations or of environmental interest. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on f

A site of communication among enterprises for supporting occupational health and safety management system.

PubMed

Velonakis, E; Mantas, J; Mavrikakis, I

2006-01-01

The occupational health and safety management constitutes a field of increasing interest. Institutions in cooperation with enterprises make synchronized efforts to initiate quality management systems to this field. Computer networks can offer such services via TCP/IP which is a reliable protocol for workflow management between enterprises and institutions. A design of such network is based on several factors in order to achieve defined criteria and connectivity with other networks. The network will be consisted of certain nodes responsible to inform executive persons on Occupational Health and Safety. A web database has been planned for inserting and searching documents, for answering and processing questionnaires. The submission of files to a server and the answers to questionnaires through the web help the experts to make corrections and improvements on their activities. Based on the requirements of enterprises we have constructed a web file server. We submit files in purpose users could retrieve the files which need. The access is limited to authorized users and digital watermarks authenticate and protect digital objects. The Health and Safety Management System follows ISO 18001. The implementation of it, through the web site is an aim. The all application is developed and implemented on a pilot basis for the health services sector. It is all ready installed within a hospital, supporting health and safety management among different departments of the hospital and allowing communication through WEB with other hospitals.

DPS Planetary Science Graduate Programs Database for Students and Advisors

NASA Astrophysics Data System (ADS)

Klassen, David R.; Roman, Anthony; Meinke, Bonnie K.

2017-10-01

Planetary science is a topic that covers an extremely diverse set of disciplines; planetary scientists are typically housed in a departments spanning a wide range of disciplines. As such it is difficult for undergraduate students to find programs that will give them a degree and research experience in our field as Department of Planetary Science is a rare sighting, indeed. Not only can this overwhelm even the most determined student, it can even be difficult for many undergraduate advisers.Because of this, the DPS Education committee decided several years ago that it should have an online resource that could help undergraduate students find graduate programs that could lead to a PhD with a focus in planetary science. It began in 2013 as a static page of information and evolved from there to a database-driven web site. Visitors can browse the entire list of programs or create a subset listing based on several filters. The site should be of use not only to undergraduates looking for programs, but also for advisers looking to help their students decide on their future plans. We present here a walk-through of the basic features as well as some usage statistics from the collected web site analytics. We ask for community feedback on additional features to make the system more usable for them. We also call upon those mentoring and advising undergraduates to use this resource, and for program admission chairs to continue to review their entry and provide us with the most up-to-date information.The URL for our site is http://dps.aas.org/education/graduate-schools.

HIV Molecular Immunology 2015

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

Yusim, Karina; Korber, Bette Tina; Brander, Christian

The scope and purpose of the HIV molecular immunology database: HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2015 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/ content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and bindingmore » sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interface on our web site at http:// www.hiv.lanl.gov/content/immunology.« less

The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience

PubMed Central

Akil, Huda; Ascoli, Giorgio A.; Bowden, Douglas M.; Bug, William; Donohue, Duncan E.; Goldberg, David H.; Grafstein, Bernice; Grethe, Jeffrey S.; Gupta, Amarnath; Halavi, Maryam; Kennedy, David N.; Marenco, Luis; Martone, Maryann E.; Miller, Perry L.; Müller, Hans-Michael; Robert, Adrian; Shepherd, Gordon M.; Sternberg, Paul W.; Van Essen, David C.; Williams, Robert W.

2009-01-01

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience’s Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line. PMID:18946742

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

The neuroscience information framework: a data and knowledge environment for neuroscience.

PubMed

Gardner, Daniel; Akil, Huda; Ascoli, Giorgio A; Bowden, Douglas M; Bug, William; Donohue, Duncan E; Goldberg, David H; Grafstein, Bernice; Grethe, Jeffrey S; Gupta, Amarnath; Halavi, Maryam; Kennedy, David N; Marenco, Luis; Martone, Maryann E; Miller, Perry L; Müller, Hans-Michael; Robert, Adrian; Shepherd, Gordon M; Sternberg, Paul W; Van Essen, David C; Williams, Robert W

2008-09-01

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience's Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov , http://neurogateway.org , and other sites as they come on line.

Ocean Drilling Program: Janus Web Database

Science.gov Websites

in Janus Data Types and Examples Leg 199, sunrise. Janus Web Database ODP and IODP data are stored in as time permits (see Database Overview for available data). Data are available to everyone. There are

Empirical studies assessing the quality of health information for consumers on the world wide web: a systematic review.

PubMed

Eysenbach, Gunther; Powell, John; Kuss, Oliver; Sa, Eun-Ryoung

The quality of consumer health information on the World Wide Web is an important issue for medicine, but to date no systematic and comprehensive synthesis of the methods and evidence has been performed. To establish a methodological framework on how quality on the Web is evaluated in practice, to determine the heterogeneity of the results and conclusions, and to compare the methodological rigor of these studies, to determine to what extent the conclusions depend on the methodology used, and to suggest future directions for research. We searched MEDLINE and PREMEDLINE (1966 through September 2001), Science Citation Index (1997 through September 2001), Social Sciences Citation Index (1997 through September 2001), Arts and Humanities Citation Index (1997 through September 2001), LISA (1969 through July 2001), CINAHL (1982 through July 2001), PsychINFO (1988 through September 2001), EMBASE (1988 through June 2001), and SIGLE (1980 through June 2001). We also conducted hand searches, general Internet searches, and a personal bibliographic database search. We included published and unpublished empirical studies in any language in which investigators searched the Web systematically for specific health information, evaluated the quality of Web sites or pages, and reported quantitative results. We screened 7830 citations and retrieved 170 potentially eligible full articles. A total of 79 distinct studies met the inclusion criteria, evaluating 5941 health Web sites and 1329 Web pages, and reporting 408 evaluation results for 86 different quality criteria. Two reviewers independently extracted study characteristics, medical domains, search strategies used, methods and criteria of quality assessment, results (percentage of sites or pages rated as inadequate pertaining to a quality criterion), and quality and rigor of study methods and reporting. Most frequently used quality criteria used include accuracy, completeness, readability, design, disclosures, and references provided. Fifty-five studies (70%) concluded that quality is a problem on the Web, 17 (22%) remained neutral, and 7 studies (9%) came to a positive conclusion. Positive studies scored significantly lower in search (P =.02) and evaluation (P =.04) methods. Due to differences in study methods and rigor, quality criteria, study population, and topic chosen, study results and conclusions on health-related Web sites vary widely. Operational definitions of quality criteria are needed.

Solution Kinetics Database on the Web

National Institute of Standards and Technology Data Gateway

SRD 40 NDRL/NIST Solution Kinetics Database on the Web (Web, free access)   Data for free radical processes involving primary radicals from water, inorganic radicals and carbon-centered radicals in solution, and singlet oxygen and organic peroxyl radicals in various solvents.

The Génolevures database.

PubMed

Martin, Tiphaine; Sherman, David J; Durrens, Pascal

2011-01-01

The Génolevures online database (URL: http://www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several campaigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedicated to large-scale comparison of these genomes, storing not only the different chromosomal elements detected in the sequences, but also the logical relations between them. The database is divided into a public part, accessible to anyone through Internet, and a private part where the Consortium members make genome annotations with our Magus annotation system; this system is used to annotate several related genomes in parallel. The public database is widely consulted and offers structured data, organized using a REST web site architecture that allows for automated requests. The implementation of the database, as well as its associated tools and methods, is evolving to cope with the influx of genome sequences produced by Next Generation Sequencing (NGS). Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Development of web tools to disseminate space geodesy data-related products

NASA Astrophysics Data System (ADS)

Soudarin, Laurent; Ferrage, Pascale; Mezerette, Adrien

2015-04-01

In order to promote the products of the DORIS system, the French Space Agency CNES has developed and implemented on the web site of the International DORIS Service (IDS) a set of plot tools to interactively build and display time series of site positions, orbit residuals and terrestrial parameters (scale, geocenter). An interactive global map is also available to select sites, and to get access to their information. Besides the products provided by the CNES Orbitography Team and the IDS components, these tools allow comparing time evolutions of coordinates for collocated DORIS and GNSS stations, thanks to the collaboration with the Terrestrial Frame Combination Center of the International GNSS Service (IGS). A database was created to improve robustness and efficiency of the tools, with the objective to propose a complete web service to foster data exchange with the other geodetic services of the International Association of Geodesy (IAG). The possibility to visualize and compare position time series of the four main space geodetic techniques DORIS, GNSS, SLR and VLBI is already under way at the French level. A dedicated version of these web tools has been developed for the French Space Geodesy Research Group (GRGS). It will give access to position time series provided by the GRGS Analysis Centers involved in DORIS, GNSS, SLR and VLBI data processing for the realization of the International Terrestrial Reference Frame. In this presentation, we will describe the functionalities of these tools, and we will address some aspects of the time series (content, format).

A Database of Historical Information on Landslides and Floods in Italy

NASA Astrophysics Data System (ADS)

Guzzetti, F.; Tonelli, G.

2003-04-01

For the past 12 years we have maintained and updated a database of historical information on landslides and floods in Italy, known as the National Research Council's AVI (Damaged Urban Areas) Project archive. The database was originally designed to respond to a specific request of the Minister of Civil Protection, and was aimed at helping the regional assessment of landslide and flood risk in Italy. The database was first constructed in 1991-92 to cover the period 1917 to 1990. Information of damaging landslide and flood event was collected by searching archives, by screening thousands of newspaper issues, by reviewing the existing technical and scientific literature on landslides and floods in Italy, and by interviewing landslide and flood experts. The database was then updated chiefly through the analysis of hundreds of newspaper articles, and it now covers systematically the period 1900 to 1998, and non-systematically the periods 1900 to 1916 and 1999 to 2002. Non systematic information on landslide and flood events older than 20th century is also present in the database. The database currently contains information on more than 32,000 landslide events occurred at more than 25,700 sites, and on more than 28,800 flood events occurred at more than 15,600 sites. After a brief outline of the history and evolution of the AVI Project archive, we present and discuss: (a) the present structure of the database, including the hardware and software solutions adopted to maintain, manage, use and disseminate the information stored in the database, (b) the type and amount of information stored in the database, including an estimate of its completeness, and (c) examples of recent applications of the database, including a web-based GIS systems to show the location of sites historically affected by landslides and floods, and an estimate of geo-hydrological (i.e., landslide and flood) risk in Italy based on the available historical information.

Web Content Accessibility of Consumer Health Information Web Sites for People with Disabilities: A Cross Sectional Evaluation

PubMed Central

Parmanto, Bambang

2004-01-01

Background The World Wide Web (WWW) has become an increasingly essential resource for health information consumers. The ability to obtain accurate medical information online quickly, conveniently and privately provides health consumers with the opportunity to make informed decisions and participate actively in their personal care. Little is known, however, about whether the content of this online health information is equally accessible to people with disabilities who must rely on special devices or technologies to process online information due to their visual, hearing, mobility, or cognitive limitations. Objective To construct a framework for an automated Web accessibility evaluation; to evaluate the state of accessibility of consumer health information Web sites; and to investigate the possible relationships between accessibility and other features of the Web sites, including function, popularity and importance. Methods We carried out a cross-sectional study of the state of accessibility of health information Web sites to people with disabilities. We selected 108 consumer health information Web sites from the directory service of a Web search engine. A measurement framework was constructed to automatically measure the level of Web Accessibility Barriers (WAB) of Web sites following Web accessibility specifications. We investigated whether there was a difference between WAB scores across various functional categories of the Web sites, and also evaluated the correlation between the WAB and Alexa traffic rank and Google Page Rank of the Web sites. Results We found that none of the Web sites we looked at are completely accessible to people with disabilities, i.e., there were no sites that had no violation of Web accessibility rules. However, governmental and educational health information Web sites do exhibit better Web accessibility than the other categories of Web sites (P < 0.001). We also found that the correlation between the WAB score and the popularity of a Web site is statistically significant (r = 0.28, P < 0.05), although there is no correlation between the WAB score and the importance of the Web sites (r = 0.15, P = 0.111). Conclusions Evaluation of health information Web sites shows that no Web site scrupulously abides by Web accessibility specifications, even for entities mandated under relevant laws and regulations. Government and education Web sites show better performance than Web sites among other categories. Accessibility of a Web site may have a positive impact on its popularity in general. However, the Web accessibility of a Web site may not have a significant relationship with its importance on the Web. PMID:15249268

SeedVicious: Analysis of microRNA target and near-target sites.

PubMed

Marco, Antonio

2018-01-01

Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. Among other novel features, seedVicious can compute evolutionary gains/losses of target sites using maximum parsimony, and also detect near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation. Some analyses suggest that near-target sites may also be functional sites, although there is no conclusive evidence for that, and they may actually be target alleles segregating in a population. SeedVicious does not aim to outperform but to complement existing microRNA prediction tools. For instance, the precision of TargetScan is almost doubled (from 11% to ~20%) when we filter predictions by the distance between target sites using this program. Interestingly, two adjacent canonical target sites are more likely to be present in bona fide target transcripts than pairs of target sites at slightly longer distances. The software is written in Perl and runs on 64-bit Unix computers (Linux and MacOS X). Users with no computing experience can also run the program in a dedicated web-server by uploading custom data, or browse pre-computed predictions. SeedVicious and its associated web-server and database (SeedBank) are distributed under the GPL/GNU license.

Motivated Proteins: A web application for studying small three-dimensional protein motifs

PubMed Central

Leader, David P; Milner-White, E James

2009-01-01

Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema. PMID:19210785

Groundwater levels for selected wells in Upper Kittitas County, Washington

USGS Publications Warehouse

Fasser, E.T.; Julich, R.J.

2011-01-01

Groundwater levels for selected wells in Upper Kittitas County, Washington, are presented on an interactive, web-based map to document the spatial distribution of groundwater levels in the study area measured during spring 2011. Groundwater-level data and well information were collected by the U.S. Geological Survey using standard techniques and are stored in the U.S. Geological Survey National Water Information System, Groundwater Site-Inventory database.

78 FR 8154 - Request for Comment: Input on Recommendations from the Council of Councils Working Group on Use...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-05

... Research on January 22, 2013. The report is posted on the NIH Web site at http://dpcpsi.nih.gov/council..., March 23, 2013, via the comment database at http://grants.nih.gov/grants/rfi/rfi.cfm?ID=31 . In the interim, NIH will continue to apply its policy on Research Involving Chimpanzees (see NOT-OD-12-025; http...

A Primer on E-Government: Sectors, Stages, Opportunities, and Challenges of Online Governance

DTIC Science & Technology

2003-01-28

government. Some observers define e-government in terms of specific actions such as using a kiosk to receive job information, or applying for Social ...participation, and governance by transforming internal and external relationships through technology, the Internet, and new media .” E-government...applying for Social Security benefits through a web site, or creating shared databases for multiple agencies, as examples. Other observers define e

HONselect: multilingual assistant search engine operated by a concept-based interface system to decentralized heterogeneous sources.

PubMed

Boyer, C; Baujard, V; Scherrer, J R

2001-01-01

Any new user to the Internet will think that to retrieve the relevant document is an easy task especially with the wealth of sources available on this medium, but this is not the case. Even experienced users have difficulty formulating the right query for making the most of a search tool in order to efficiently obtain an accurate result. The goal of this work is to reduce the time and the energy necessary in searching and locating medical and health information. To reach this goal we have developed HONselect [1]. The aim of HONselect is not only to improve efficiency in retrieving documents but to respond to an increased need for obtaining a selection of relevant and accurate documents from a breadth of various knowledge databases including scientific bibliographical references, clinical trials, daily news, multimedia illustrations, conferences, forum, Web sites, clinical cases, and others. The authors based their approach on the knowledge representation using the National Library of Medicine's Medical Subject Headings (NLM, MeSH) vocabulary and classification [2,3]. The innovation is to propose a multilingual "one-stop searching" (one Web interface to databases currently in English, French and German) with full navigational and connectivity capabilities. The user may choose from a given selection of related terms the one that best suit his search, navigate in the term's hierarchical tree, and access directly to a selection of documents from high quality knowledge suppliers such as the MEDLINE database, the NLM's ClinicalTrials.gov server, the NewsPage's daily news, the HON's media gallery, conference listings and MedHunt's Web sites [4, 5, 6, 7, 8, 9]. HONselect, developed by HON, a non-profit organisation [10], is a free online available multilingual tool based on the MeSH thesaurus to index, select, retrieve and display accurate, up to date, high-level and quality documents.

ATLAS, CMS and new challenges for public communication

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

Taylor, Lucas; Barney, David; Goldfarb, Steven

On 30 March 2010 the first high-energy collisions brought the LHC experiments into the era of research and discovery. Millions of viewers worldwide tuned in to the webcasts and followed the news via Web 2.0 tools, such as blogs, Twitter, and Facebook, with 205,000 unique visitors to CERN's Web site. Media coverage at the experiments and in institutes all over the world yielded more than 2,200 news items including 800 TV broadcasts. We describe the new multimedia communications challenges, due to the massive public interest in the LHC programme, and the corresponding responses of the ATLAS and CMS experiments, inmore » the areas of Web 2.0 tools, multimedia, webcasting, videoconferencing, and collaborative tools. We discuss the strategic convergence of the two experiments' communications services, information systems and public database of outreach material.« less

ATLAS, CMS and New Challenges for Public Communication

NASA Astrophysics Data System (ADS)

Taylor, Lucas; Barney, David; Goldfarb, Steven

2011-12-01

On 30 March 2010 the first high-energy collisions brought the LHC experiments into the era of research and discovery. Millions of viewers worldwide tuned in to the webcasts and followed the news via Web 2.0 tools, such as blogs, Twitter, and Facebook, with 205,000 unique visitors to CERN's Web site. Media coverage at the experiments and in institutes all over the world yielded more than 2,200 news items including 800 TV broadcasts. We describe the new multimedia communications challenges, due to the massive public interest in the LHC programme, and the corresponding responses of the ATLAS and CMS experiments, in the areas of Web 2.0 tools, multimedia, webcasting, videoconferencing, and collaborative tools. We discuss the strategic convergence of the two experiments' communications services, information systems and public database of outreach material.

Discrepancies among Scopus, Web of Science, and PubMed coverage of funding information in medical journal articles.

PubMed

Kokol, Peter; Vošner, Helena Blažun

2018-01-01

The overall aim of the present study was to compare the coverage of existing research funding information for articles indexed in Scopus, Web of Science, and PubMed databases. The numbers of articles with funding information published in 2015 were identified in the three selected databases and compared using bibliometric analysis of a sample of twenty-eight prestigious medical journals. Frequency analysis of the number of articles with funding information showed statistically significant differences between Scopus, Web of Science, and PubMed databases. The largest proportion of articles with funding information was found in Web of Science (29.0%), followed by PubMed (14.6%) and Scopus (7.7%). The results show that coverage of funding information differs significantly among Scopus, Web of Science, and PubMed databases in a sample of the same medical journals. Moreover, we found that, currently, funding data in PubMed is more difficult to obtain and analyze compared with that in the other two databases.

BAID: The Barrow Area Information Database - an interactive web mapping portal and cyberinfrastructure for scientific activities in the vicinity of Barrow, Alaska

NASA Astrophysics Data System (ADS)

Cody, R. P.; Kassin, A.; Gaylord, A.; Brown, J.; Tweedie, C. E.

2012-12-01

The Barrow area of northern Alaska is one of the most intensely researched locations in the Arctic. The Barrow Area Information Database (BAID, www.baidims.org) is a cyberinfrastructure (CI) that details much of the historic and extant research undertaken within in the Barrow region in a suite of interactive web-based mapping and information portals (geobrowsers). The BAID user community and target audience for BAID is diverse and includes research scientists, science logisticians, land managers, educators, students, and the general public. BAID contains information on more than 9,600 Barrow area research sites that extend back to the 1940's and more than 640 remote sensing images and geospatial datasets. In a web-based setting, users can zoom, pan, query, measure distance, and save or print maps and query results. Data are described with metadata that meet Federal Geographic Data Committee standards and are archived at the University Corporation for Atmospheric Research Earth Observing Laboratory (EOL) where non-proprietary BAID data can be freely downloaded. BAID has been used to: Optimize research site choice; Reduce duplication of science effort; Discover complementary and potentially detrimental research activities in an area of scientific interest; Re-establish historical research sites for resampling efforts assessing change in ecosystem structure and function over time; Exchange knowledge across disciplines and generations; Facilitate communication between western science and traditional ecological knowledge; Provide local residents access to science data that facilitates adaptation to arctic change; (and) Educate the next generation of environmental and computer scientists. This poster describes key activities that will be undertaken over the next three years to provide BAID users with novel software tools to interact with a current and diverse selection of information and data about the Barrow area. Key activities include: 1. Collecting data on research activities, generating geospatial data, and providing mapping support. 2. Maintaining, updating and innovating the existing suite of BAID geobrowsers. 3. Maintaining and updating aging server hardware supporting BAID. 4. Adding interoperability with other CI using workflows, controlled vocabularies and web services. 5. Linking BAID to data archives at the National Snow and Ice Data Center (NSIDC). 6. Developing a wireless sensor network that provides web based interaction with near-real time climate and other data. 7. Training next generation of environmental and computer scientists and conducting outreach.

A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

USDA-ARS?s Scientific Manuscript database

The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

Collection Fusion Using Bayesian Estimation of a Linear Regression Model in Image Databases on the Web.

ERIC Educational Resources Information Center

Kim, Deok-Hwan; Chung, Chin-Wan

2003-01-01

Discusses the collection fusion problem of image databases, concerned with retrieving relevant images by content based retrieval from image databases distributed on the Web. Focuses on a metaserver which selects image databases supporting similarity measures and proposes a new algorithm which exploits a probabilistic technique using Bayesian…

The Web-Database Connection Tools for Sharing Information on the Campus Intranet.

ERIC Educational Resources Information Center

Thibeault, Nancy E.

This paper evaluates four tools for creating World Wide Web pages that interface with Microsoft Access databases: DB Gateway, Internet Database Assistant (IDBA), Microsoft Internet Database Connector (IDC), and Cold Fusion. The system requirements and features of each tool are discussed. A sample application, "The Virtual Help Desk"…

An Overview of ARL’s Multimodal Signatures Database and Web Interface

DTIC Science & Technology

2007-12-01

ActiveX components, which hindered distribution due to license agreements and run-time license software to use such components. g. Proprietary...Overview The database consists of multimodal signature data files in the HDF5 format. Generally, each signature file contains all the ancillary...only contains information in the database, Web interface, and signature files that is releasable to the public. The Web interface consists of static

Analysis and Development of a Web-Enabled Planning and Scheduling Database Application

DTIC Science & Technology

2013-09-01

establishes an entity—relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web- enabled interface for...development, develop, design, process, re- engineering, reengineering, MySQL , structured query language, SQL, myPHPadmin. 15. NUMBER OF PAGES 107 16...relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web-enabled interface for the population of

Vision science literature of Nepal in the database "Web of Science".

PubMed

Risal, S; Prasad, H N

2012-01-01

Vision Science is considered to be a quite developed discipline in Nepal, with much research currently in progress. Though the results of these endeavors are published in scientific journals, formal citation analyses have not been performed on works contributed by Nepalese vision scientists. To study Nepal's contribution to vision science literature in the database "Web of Science". The primary data source of this paper was Web of Science, a citation database of Thomas Reuters. All bibliometric analyses were performed with the help of Web of Science analysis service. In the current database of vision science literature, Nepalese authors contributed 112 publications to Web of Science, 95 of which were original articles. Pokharel GP had the highest number of citations among contributing authors of Nepal. Hennig A contributed the highest number of article as a first author. The Nepal Eye Hospital contributed the highest number of articles as an institution to the field of Vision Science. Currently, only two journals from Nepal including Journal of Nepal Medical Association (JAMA) are indexed in the Web of Science database (Sieving, 2012). To evaluate the total productivity of vision science literature from Nepal, total publication counts from national journals and articles indexed in other databases such as PubMed and Scopus must also be considered. © NEPjOPH.

Expedition Memory: Towards Agent-based Web Services for Creating and Using Mars Exploration Data.

NASA Technical Reports Server (NTRS)

Clancey, William J.; Sierhuis, Maarten; Briggs, Geoff; Sims, Mike

2005-01-01

Explorers ranging over kilometers of rugged, sometimes "feature-less" terrain for over a year could be overwhelmed by tracking and sharing what they have done and learned. An automated system based on the existing Mobile Agents design [ I ] and Mars Exploration Rover experience [2], could serve as an "expedition memory" that would be indexed by voice as wel1 as a web interface, linking people, places, activities, records (voice notes, photographs, samples). and a descriptive scientific ontology. This database would be accessible during EVAs by astronauts, annotated by the remote science team, linked to EVA plans, and allow cross indexing between sites and expeditions. We consider the basic problem, our philosophical approach, technical methods, and uses of the expedition memory for facilitating long-term collaboration between Mars crews and Earth support teams. We emphasize that a "memory" does not mean a database per se, but an interactive service that combines different resources, and ultimately could be like a helpful librarian.

Telemedicine information analysis center.

PubMed

Zajtchuk, Joan T; Zajtchuk, Russ; Petrovic, Joseph J; Gutz, Ryan P; Walrath, Benjamin D

2004-01-01

Congress mandated a pilot project to demonstrate the feasibility of establishing a Department of Defense (DoD) telemedicine information analysis center (TIAC). The project developed a medical information support system to show the core capabilities of a TIAC. The productivity and effectiveness of telemedicine researchers and clinical practitioners can be enhanced by the existence of an information analysis center (IACs) devoted to the collection, analysis, synthesis, and dissemination of worldwide scientific and technical information related to the field of telemedicine. The work conducted under the TIAC pilot project establishes the basic IAC functions and assesses the utility of the TIAC to the military medical departments. The pilot project capabilities are Web-based and include: (1) applying the science of classification (taxonomy) to telemedicine to identify key words; (2) creating a relational database of this taxonomy to a bibliographic database using these key words; (3) developing and disseminating information via a public TIAC Web site; (4) performing a specific baseline technical area task for the U.S. Army Medical Command; and (5) providing analyses by subject matter experts.

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation

PubMed Central

Veal, Colin D.; Xu, Hang; Reekie, Katherine; Free, Robert; Hardwick, Robert J.; McVey, David; Brookes, Anthony J.; Hollox, Edward J.; Talbot, Christopher J.

2013-01-01

Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design. Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT. Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org). Contact: cjt14@le.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23742985

SU-F-P-10: A Web-Based Radiation Safety Relational Database Module for Regulatory Compliance

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

Rosen, C; Ramsay, B; Konerth, S

Purpose: Maintaining compliance with Radioactive Materials Licenses is inherently a time-consuming task requiring focus and attention to detail. Staff tasked with these responsibilities, such as the Radiation Safety Officer and associated personnel must retain disparate records for eventual placement into one or more annual reports. Entering results and records in a relational database using a web browser as the interface, and storing that data in a cloud-based storage site, removes procedural barriers. The data becomes more adaptable for mining and sharing. Methods: Web-based code was written utilizing the web framework Django, written in Python. Additionally, the application utilizes JavaScript formore » front-end interaction, SQL, HTML and CSS. Quality assurance code testing is performed in a sequential style, and new code is only added after the successful testing of the previous goals. Separate sections of the module include data entry and analysis for audits, surveys, quality management, and continuous quality improvement. Data elements can be adapted for quarterly and annual reporting, and for immediate notification of user determined alarm settings. Results: Current advances are focusing on user interface issues, and determining the simplest manner by which to teach the user to build query forms. One solution has been to prepare library documents that a user can select or edit in place of creation a new document. Forms are being developed based upon Nuclear Regulatory Commission federal code, and will be expanded to include State Regulations. Conclusion: Establishing a secure website to act as the portal for data entry, storage and manipulation can lead to added efficiencies for a Radiation Safety Program. Access to multiple databases can lead to mining for big data programs, and for determining safety issues before they occur. Overcoming web programming challenges, a category that includes mathematical handling, is providing challenges that are being overcome.« less

Systematic Analysis of Arabidopsis Organelles and a Protein Localization Database for Facilitating Fluorescent Tagging of Full-Length Arabidopsis Proteins1[W

PubMed Central

Li, Shijun; Ehrhardt, David W.; Rhee, Seung Y.

2006-01-01

Cells are organized into a complex network of subcellular compartments that are specialized for various biological functions. Subcellular location is an important attribute of protein function. To facilitate systematic elucidation of protein subcellular location, we analyzed experimentally verified protein localization data of 1,300 Arabidopsis (Arabidopsis thaliana) proteins. The 1,300 experimentally verified proteins are distributed among 40 different compartments, with most of the proteins localized to four compartments: mitochondria (36%), nucleus (28%), plastid (17%), and cytosol (13.3%). About 19% of the proteins are found in multiple compartments, in which a high proportion (36.4%) is localized to both cytosol and nucleus. Characterization of the overrepresented Gene Ontology molecular functions and biological processes suggests that the Golgi apparatus and peroxisome may play more diverse functions but are involved in more specialized processes than other compartments. To support systematic empirical determination of protein subcellular localization using a technology called fluorescent tagging of full-length proteins, we developed a database and Web application to provide preselected green fluorescent protein insertion position and primer sequences for all Arabidopsis proteins to study their subcellular localization and to store experimentally verified protein localization images, videos, and their annotations of proteins generated using the fluorescent tagging of full-length proteins technology. The database can be searched, browsed, and downloaded using a Web browser at http://aztec.stanford.edu/gfp/. The software can also be downloaded from the same Web site for local installation. PMID:16617091

The NASA John C. Stennis Environmental Geographic Information System

NASA Technical Reports Server (NTRS)

Cohan, Tyrus; Grant, Kerry

2002-01-01

In addition to the Environmental Geographic Information System (EGIS) presentation, we will present two live demonstrations of a portion of the work being performed in support of environmental operations onsite and NASA-wide. These live demonstrations will showcase the NASA EGIS database through working versions of two software packages available from Environmental Systems Research Institute, Inc. (ESRI, Inc.): ArcIMS 3.0 and either ArcView 3.2a or ArcGIS 8.0.2. Using a standard web browser, the ArcIMS demo will allow users to access a project file containing several data layers found in the EGIS database. ArcIMS is configured so that a single computer can be used as the data server and as the user interface, which allows for maximum Internet security because the computer being used will not actually be connected to the World Wide Web. Further, being independent of the Internet, the demo will run at an increased speed. This demo will include several data layers that are specific to Stennis Space Center. The EGIS database demo is a representative portion of the entire EGIS project sent to NASA Headquarters last year. This demo contains data files that are readily available at various government agency Web sites for download. Although these files contain roads, rails, and other infrastructure details, they are generalized and at a small enough scale that they provide only a general idea of each NASA center's surroundings rather than specific details of the area.

32 CFR 701.102 - Online resources.

Code of Federal Regulations, 2010 CFR

2010-07-01

... online Web site (http://www.privacy.navy.mil). This Web site supplements this subpart and subpart G. It...) Web site (http://www.doncio.navy.mil). This Web site provides detailed guidance on PIAs. (c) DOD's PA Web site (http://www.defenselink.mil/privacy). This Web site is an excellent resource that contains a...

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.

THE NASA AMES PAH IR SPECTROSCOPIC DATABASE VERSION 2.00: UPDATED CONTENT, WEB SITE, AND ON(OFF)LINE TOOLS

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

Boersma, C.; Mattioda, A. L.; Allamandola, L. J.

A significantly updated version of the NASA Ames PAH IR Spectroscopic Database, the first major revision since its release in 2010, is presented. The current version, version 2.00, contains 700 computational and 75 experimental spectra compared, respectively, with 583 and 60 in the initial release. The spectra span the 2.5-4000 μm (4000-2.5 cm{sup -1}) range. New tools are available on the site that allow one to analyze spectra in the database and compare them with imported astronomical spectra as well as a suite of IDL object classes (a collection of programs utilizing IDL's object-oriented programming capabilities) that permit offline analysismore » called the AmesPAHdbIDLSuite. Most noteworthy among the additions are the extension of the computational spectroscopic database to include a number of significantly larger polycyclic aromatic hydrocarbons (PAHs), the ability to visualize the molecular atomic motions corresponding to each vibrational mode, and a new tool that allows one to perform a non-negative least-squares fit of an imported astronomical spectrum with PAH spectra in the computational database. Finally, a methodology is described in the Appendix, and implemented using the AmesPAHdbIDLSuite, that allows the user to enforce charge balance during the fitting procedure.« less

Development of a functional, internet-accessible department of surgery outcomes database.

PubMed

Newcomb, William L; Lincourt, Amy E; Gersin, Keith; Kercher, Kent; Iannitti, David; Kuwada, Tim; Lyons, Cynthia; Sing, Ronald F; Hadzikadic, Mirsad; Heniford, B Todd; Rucho, Susan

2008-06-01

The need for surgical outcomes data is increasing due to pressure from insurance companies, patients, and the need for surgeons to keep their own "report card". Current data management systems are limited by inability to stratify outcomes based on patients, surgeons, and differences in surgical technique. Surgeons along with research and informatics personnel from an academic, hospital-based Department of Surgery and a state university's Department of Information Technology formed a partnership to develop a dynamic, internet-based, clinical data warehouse. A five-component model was used: data dictionary development, web application creation, participating center education and management, statistics applications, and data interpretation. A data dictionary was developed from a list of data elements to address needs of research, quality assurance, industry, and centers of excellence. A user-friendly web interface was developed with menu-driven check boxes, multiple electronic data entry points, direct downloads from hospital billing information, and web-based patient portals. Data were collected on a Health Insurance Portability and Accountability Act-compliant server with a secure firewall. Protected health information was de-identified. Data management strategies included automated auditing, on-site training, a trouble-shooting hotline, and Institutional Review Board oversight. Real-time, daily, monthly, and quarterly data reports were generated. Fifty-eight publications and 109 abstracts have been generated from the database during its development and implementation. Seven national academic departments now use the database to track patient outcomes. The development of a robust surgical outcomes database requires a combination of clinical, informatics, and research expertise. Benefits of surgeon involvement in outcomes research include: tracking individual performance, patient safety, surgical research, legal defense, and the ability to provide accurate information to patient and payers.

The National Land Cover Database

USGS Publications Warehouse

Homer, Collin G.; Fry, Joyce A.; Barnes, Christopher A.

2012-01-01

The National Land Cover Database (NLCD) serves as the definitive Landsat-based, 30-meter resolution, land cover database for the Nation. NLCD provides spatial reference and descriptive data for characteristics of the land surface such as thematic class (for example, urban, agriculture, and forest), percent impervious surface, and percent tree canopy cover. NLCD supports a wide variety of Federal, State, local, and nongovernmental applications that seek to assess ecosystem status and health, understand the spatial patterns of biodiversity, predict effects of climate change, and develop land management policy. NLCD products are created by the Multi-Resolution Land Characteristics (MRLC) Consortium, a partnership of Federal agencies led by the U.S. Geological Survey. All NLCD data products are available for download at no charge to the public from the MRLC Web site: http://www.mrlc.gov.

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2014-01-15

Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

Analysis of pathology department Web sites and practical recommendations.

PubMed

Nero, Christopher; Dighe, Anand S

2008-09-01

There are numerous customers for pathology departmental Web sites, including pathology department staff, clinical staff, residency applicants, job seekers, and other individuals outside the department seeking department information. Despite the increasing importance of departmental Web sites as a means of distributing information, no analysis has been done to date of the content and usage of pathology department Web sites. In this study, we analyzed pathology department Web sites to examine the elements present on each site and to evaluate the use of search technology on these sites. Further, we examined the usage patterns of our own departmental Internet and internet Web sites to better understand the users of pathology Web sites. We reviewed selected departmental pathology Web sites and analyzed their content and functionality. Our institution's departmental pathology Web sites were modified to enable detailed information to be stored regarding users and usage patterns, and that information was analyzed. We demonstrate considerable heterogeneity in departmental Web sites with many sites lacking basic content and search features. In addition, we demonstrate that increasing the traffic of a department's informational Web sites may result in reduced phone inquiries to the laboratory. We propose recommendations for pathology department Web sites to maximize promotion of a department's mission. A departmental pathology Web site is an essential communication tool for all pathology departments, and attention to the users and content of the site can have operational impact.

A targeted e-learning program for surgical trainees to enhance patient safety in preventing surgical infection.

PubMed

McHugh, Seamus Mark; Corrigan, Mark; Dimitrov, Borislav; Cowman, Seamus; Tierney, Sean; Humphreys, Hilary; Hill, Arnold

2010-01-01

Surgical site infection accounts for 20% of all health care-associated infections (HCAIs); however, a program incorporating the education of surgeons has yet to be established across the specialty. An audit of surgical practice in infection prevention was carried out in Beaumont Hospital from July to November 2009. An educational Web site was developed targeting deficiencies highlighted in the audit. Interactive clinical cases were constructed using PHP coding, an HTML-embedded language, and then linked to a MySQL relational database. PowerPoint tutorials were produced as online Flash audiovisual movies. An online repository of streaming videos demonstrating best practice was made available, and weekly podcasts were made available on the iTunes© store for free download. Usage of the e-learning program was assessed quantitatively over 6 weeks in May and June 2010 using the commercial company Hitslink. During the 5-month audit, deficiencies in practice were highlighted, including the timing of surgical prophylaxis (33% noncompliance) and intravascular catheter care in surgical patients (38% noncompliance regarding necessity). Over the 6-week assessment of the educational material, the SurgInfection.com Web pages were accessed more than 8000 times; 77.9% of the visitors were from Ireland. The most commonly accessed modality was the repository with interactive clinical cases, accounting for 3463 (43%) of the Web site visits. The average user spent 57 minutes per visit, with 30% of them visiting the Web site multiple times. Interactive virtual cases mirroring real-life clinical scenarios are likely to be successful as an e-learning modality. User-friendly interfaces and 24-hour accessibility will increases uptake by surgical trainees.

Development of a medical module for disaster information systems.

PubMed

Calik, Elif; Atilla, Rıdvan; Kaya, Hilal; Aribaş, Alirıza; Cengiz, Hakan; Dicle, Oğuz

2014-01-01

This study aims to improve a medical module which provides a real-time medical information flow about pre-hospital processes that gives health care in disasters; transferring, storing and processing the records that are in electronic media and over internet as a part of disaster information systems. In this study which is handled within the frame of providing information flow among professionals in a disaster case, to supply the coordination of healthcare team and transferring complete information to specified people at real time, Microsoft Access database and SQL query language were used to inform database applications. System was prepared on Microsoft .Net platform using C# language. Disaster information system-medical module was designed to be used in disaster area, field hospital, nearby hospitals, temporary inhabiting areas like tent city, vehicles that are used for dispatch, and providing information flow between medical officials and data centres. For fast recording of the disaster victim data, accessing to database which was used by health care professionals was provided (or granted) among analysing process steps and creating minimal datasets. Database fields were created in the manner of giving opportunity to enter new data and search old data which is recorded before disaster. Web application which provides access such as data entry to the database and searching towards the designed interfaces according to the login credentials access level. In this study, homepage and users' interfaces which were built on database in consequence of system analyses were provided with www.afmedinfo.com web site to the user access. With this study, a recommendation was made about how to use disaster-based information systems in the field of health. Awareness has been developed about the fact that disaster information system should not be perceived only as an early warning system. Contents and the differences of the health care practices of disaster information systems were revealed. A web application was developed supplying a link between the user and the database to make date entry and data query practices by the help of the developed interfaces.

The Great War: Online Resources.

ERIC Educational Resources Information Center

Duncanson, Bruce

2002-01-01

Presents an annotated bibliography of Web sites about World War I. Includes: (1) general Web sites; (2) Web sites with information during the war; (3) Web sites with information about post-World War I; (4) Web sites that provide photos, sound files of speeches, and propaganda posters; and (5) Web sites with lesson plans. (CMK)

Dealing with an information overload of health science data: structured utilisation of libraries, distributed knowledge in databases and Web content.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Rieger, Joerg; Meyer, Michael

2006-01-01

The organizational structures of web contents and electronic information resources must adapt to the demands of a growing volume of information and user requirements. Otherwise the information society will be threatened by disinformation. The biomedical sciences are especially vulnerable in this regard, since they are strongly oriented toward text-based knowledge sources. Here sustainable improvement can only be achieved by using a comprehensive, integrated approach that not only includes data management but also specifically incorporates the editorial processes, including structuring information sources and publication. The technical resources needed to effectively master these tasks are already available in the form of the data standards and tools of the Semantic Web. They include Rich Site Summaries (RSS), which have become an established means of distributing and syndicating conventional news messages and blogs. They can also provide access to the contents of the previously mentioned information sources, which are conventionally classified as 'deep web' content.

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

PubMed

Huang, Yu S; Horton, Matthew; Vilhjálmsson, Bjarni J; Seren, Umit; Meng, Dazhe; Meyer, Christopher; Ali Amer, Muhammad; Borevitz, Justin O; Bergelson, Joy; Nordborg, Magnus

2011-01-01

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

Web data mining

NASA Astrophysics Data System (ADS)

Wibonele, Kasanda J.; Zhang, Yanqing

2002-03-01

A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

Mining a Web Citation Database for Author Co-Citation Analysis.

ERIC Educational Resources Information Center

He, Yulan; Hui, Siu Cheung

2002-01-01

Proposes a mining process to automate author co-citation analysis based on the Web Citation Database, a data warehouse for storing citation indices of Web publications. Describes the use of agglomerative hierarchical clustering for author clustering and multidimensional scaling for displaying author cluster maps, and explains PubSearch, a…

Latest developments for the IAGOS database: Interoperability and metadata

NASA Astrophysics Data System (ADS)

Boulanger, Damien; Gautron, Benoit; Thouret, Valérie; Schultz, Martin; van Velthoven, Peter; Broetz, Bjoern; Rauthe-Schöch, Armin; Brissebrat, Guillaume

2014-05-01

In-service Aircraft for a Global Observing System (IAGOS, http://www.iagos.org) aims at the provision of long-term, frequent, regular, accurate, and spatially resolved in situ observations of the atmospheric composition. IAGOS observation systems are deployed on a fleet of commercial aircraft. The IAGOS database is an essential part of the global atmospheric monitoring network. Data access is handled by open access policy based on the submission of research requests which are reviewed by the PIs. Users can access the data through the following web sites: http://www.iagos.fr or http://www.pole-ether.fr as the IAGOS database is part of the French atmospheric chemistry data centre ETHER (CNES and CNRS). The database is in continuous development and improvement. In the framework of the IGAS project (IAGOS for GMES/COPERNICUS Atmospheric Service), major achievements will be reached, such as metadata and format standardisation in order to interoperate with international portals and other databases, QA/QC procedures and traceability, CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) data integration within the central database, and the real-time data transmission. IGAS work package 2 aims at providing the IAGOS data to users in a standardized format including the necessary metadata and information on data processing, data quality and uncertainties. We are currently redefining and standardizing the IAGOS metadata for interoperable use within GMES/Copernicus. The metadata are compliant with the ISO 19115, INSPIRE and NetCDF-CF conventions. IAGOS data will be provided to users in NetCDF or NASA Ames format. We also are implementing interoperability between all the involved IAGOS data services, including the central IAGOS database, the former MOZAIC and CARIBIC databases, Aircraft Research DLR database and the Jülich WCS web application JOIN (Jülich OWS Interface) which combines model outputs with in situ data for intercomparison. The optimal data transfer protocol is being investigated to insure the interoperability. To facilitate satellite and model validation, tools will be made available for co-location and comparison with IAGOS. We will enhance the JOIN application in order to properly display aircraft data as vertical profiles and along individual flight tracks and to allow for graphical comparison to model results that are accessible through interoperable web services, such as the daily products from the GMES/Copernicus atmospheric service.

Food and beverage brands that market to children and adolescents on the internet: a content analysis of branded web sites.

PubMed

Henry, Anna E; Story, Mary

2009-01-01

To identify food and beverage brand Web sites featuring designated children's areas, assess marketing techniques present on those industry Web sites, and determine nutritional quality of branded food items marketed to children. Systematic content analysis of food and beverage brand Web sites and nutrient analysis of food and beverages advertised on these Web sites. The World Wide Web. One-hundred thirty Internet Web sites of food and beverage brands with top media expenditures based on the America's Top 2000 Brands section of Brandweek magazine's annual "Superbrands" report. A standardized content analysis rating form to determine marketing techniques used on the food and beverage brand Web sites. Nutritional analysis of food brands was conducted. Of 130 Web sites analyzed, 48% featured designated children's areas. These Web sites featured a variety of Internet marketing techniques, including advergaming on 85% of the Web sites and interactive programs on 92% of the Web sites. Branded spokescharacters and tie-ins to other products were featured on the majority of the Web sites, as well. Few food brands (13%) with Web sites that market to children met the nutrition criteria set by the National Alliance for Nutrition and Activity. Nearly half of branded Web sites analyzed used designated children's areas to market food and beverages to children, 87% of which were of low nutritional quality. Nutrition professionals should advocate the use of advertising techniques to encourage healthful food choices for children.

The Arctic Observing Viewer: A Web-mapping Application for U.S. Arctic Observing Activities

NASA Astrophysics Data System (ADS)

Cody, R. P.; Manley, W. F.; Gaylord, A. G.; Kassin, A.; Villarreal, S.; Barba, M.; Dover, M.; Escarzaga, S. M.; Habermann, T.; Kozimor, J.; Score, R.; Tweedie, C. E.

2015-12-01

Although a great deal of progress has been made with various arctic observing efforts, it can be difficult to assess such progress when so many agencies, organizations, research groups and others are making such rapid progress over such a large expanse of the Arctic. To help meet the strategic needs of the U.S. SEARCH-AON program and facilitate the development of SAON and other related initiatives, the Arctic Observing Viewer (AOV; http://ArcticObservingViewer.org) has been developed. This web mapping application compiles detailed information pertaining to U.S. Arctic Observing efforts. Contributing partners include the U.S. NSF, USGS, ACADIS, ADIwg, AOOS, a2dc, AON, ARMAP, BAID, IASOA, INTERACT, and others. Over 7700 observation sites are currently in the AOV database and the application allows users to visualize, navigate, select, advance search, draw, print, and more. During 2015, the web mapping application has been enhanced by the addition of a query builder that allows users to create rich and complex queries. AOV is founded on principles of software and data interoperability and includes an emerging "Project" metadata standard, which uses ISO 19115-1 and compatible web services. Substantial efforts have focused on maintaining and centralizing all database information. In order to keep up with emerging technologies, the AOV data set has been structured and centralized within a relational database and the application front-end has been ported to HTML5 to enable mobile access. Other application enhancements include an embedded Apache Solr search platform which provides users with the capability to perform advance searches and an administration web based data management system that allows administrators to add, update, and delete information in real time. We encourage all collaborators to use AOV tools and services for their own purposes and to help us extend the impact of our efforts and ensure AOV complements other cyber-resources. Reinforcing dispersed but interoperable resources in this way will help to ensure improved capacities for conducting activities such as assessing the status of arctic observing efforts, optimizing logistic operations, and for quickly accessing external and project-focused web resources for more detailed information and access to scientific data and derived products.

Database of Novel and Emerging Adsorbent Materials

National Institute of Standards and Technology Data Gateway

SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

Development of a laboratory niche Web site.

PubMed

Dimenstein, Izak B; Dimenstein, Simon I

2013-10-01

This technical note presents the development of a methodological laboratory niche Web site. The "Grossing Technology in Surgical Pathology" (www.grossing-technology.com) Web site is used as an example. Although common steps in creation of most Web sites are followed, there are particular requirements for structuring the template's menu on methodological laboratory Web sites. The "nested doll principle," in which one object is placed inside another, most adequately describes the methodological approach to laboratory Web site design. Fragmentation in presenting the Web site's material highlights the discrete parts of the laboratory procedure. An optimally minimal triad of components can be recommended for the creation of a laboratory niche Web site: a main set of media, a blog, and an ancillary component (host, contact, and links). The inclusion of a blog makes the Web site a dynamic forum for professional communication. By forming links and portals, cloud computing opens opportunities for connecting a niche Web site with other Web sites and professional organizations. As an additional source of information exchange, methodological laboratory niche Web sites are destined to parallel both traditional and new forms, such as books, journals, seminars, webinars, and internal educational materials. Copyright © 2013 Elsevier Inc. All rights reserved.

Development of a large urban longitudinal HIV clinical cohort using a web-based platform to merge electronically and manually abstracted data from disparate medical record systems: technical challenges and innovative solutions

PubMed Central

Hays, Harlen; Castel, Amanda D; Subramanian, Thilakavathy; Happ, Lindsey Powers; Jaurretche, Maria; Binkley, Jeff; Kalmin, Mariah M; Wood, Kathy; Hart, Rachel

2016-01-01

Objective Electronic medical records (EMRs) are being increasingly utilized to conduct clinical and epidemiologic research in numerous fields. To monitor and improve care of HIV-infected patients in Washington, DC, one of the most severely affected urban areas in the United States, we developed a city-wide database across 13 clinical sites using electronic data abstraction and manual data entry from EMRs. Materials and Methods To develop this unique longitudinal cohort, a web-based electronic data capture system (Discovere®) was used. An Agile software development methodology was implemented across multiple EMR platforms. Clinical informatics staff worked with information technology specialists from each site to abstract data electronically from each respective site’s EMR through an extract, transform, and load process. Results Since enrollment began in 2011, more than 7000 patients have been enrolled, with longitudinal clinical data available on all patients. Data sets are produced for scientific analyses on a quarterly basis, and benchmarking reports are generated semi-annually enabling each site to compare their participants’ clinical status, treatments, and outcomes to the aggregated summaries from all other sites. Discussion Numerous technical challenges were identified and innovative solutions developed to ensure the successful implementation of the DC Cohort. Central to the success of this project was the broad collaboration established between government, academia, clinics, community, information technology staff, and the patients themselves. Conclusions Our experiences may have practical implications for researchers who seek to merge data from diverse clinical databases, and are applicable to the study of health-related issues beyond HIV. PMID:26721732

Implementing an SIG based platform of application and service for city spatial information in Shanghai

NASA Astrophysics Data System (ADS)

Yu, Bailang; Wu, Jianping

2006-10-01

Spatial Information Grid (SIG) is an infrastructure that has the ability to provide the services for spatial information according to users' needs by means of collecting, sharing, organizing and processing the massive distributed spatial information resources. This paper presents the architecture, technologies and implementation of the Shanghai City Spatial Information Application and Service System, a SIG based platform, which is an integrated platform that serves for administration, planning, construction and development of the city. In the System, there are ten categories of spatial information resources, including city planning, land-use, real estate, river system, transportation, municipal facility construction, environment protection, sanitation, urban afforestation and basic geographic information data. In addition, spatial information processing services are offered as a means of GIS Web Services. The resources and services are all distributed in different web-based nodes. A single database is created to store the metadata of all the spatial information. A portal site is published as the main user interface of the System. There are three main functions in the portal site. First, users can search the metadata and consequently acquire the distributed data by using the searching results. Second, some spatial processing web applications that developed with GIS Web Services, such as file format conversion, spatial coordinate transfer, cartographic generalization and spatial analysis etc, are offered to use. Third, GIS Web Services currently available in the System can be searched and new ones can be registered. The System has been working efficiently in Shanghai Government Network since 2005.

A Tephra Database With an Intelligent Correlation System, Mono-Inyo Volcanic Chain, CA

NASA Astrophysics Data System (ADS)

Bursik, M.; Rogova, G.

2004-12-01

We are assembling a web-accessible, relational database of information on past eruptions of the Mono-Inyo volcanic chain, eastern California. The PostgreSQL database structure follows the North American Data Model and CordLink. The database allows us to extract the features diagnostic of particular pyroclastic layers, as well as lava domes and flows. The features include depth in the section, layer thickness and internal stratigraphy, mineral assemblage, major and trace element composition, tephra componentry and granulometry, and radiocarbon age. Our working hypotheses are that 1) the database will prove useful for unraveling the complex recent volcanic history of the Mono-Inyo chain 2) aided by the use of an intelligent correlation system integrated into the database system. The Mono-Inyo chain consists of domes, craters and flows that stretch for 50 km north-south, subparallel to the Sierran range front fault system. Almost all eruptions within the chain probably occurred less than 50,000 years ago. Because of the variety of magma and eruption types, and the migration of source regions in time and space, it is nontrivial to discern patterns of behaviour. We have explored the use of multiple artificial neural networks combined within the framework of the Dempster-Shafer theory of evidence to construct a hybrid information processing system as an aid in the correlation of Mono-Inyo pyroclastic layers. It is hoped that such a system could provide information useful to discerning eruptive patterns that would otherwise be difficult to sort and categorize. In a test case on tephra layers at known sites, the intelligent correlation system was able to categorize observations correctly 96% of the time. In a test case with layers at one unknown site, and using a pairwise comparison of the unknown site with the known sites, a one-to-one correlation between the unknown site and the known sites was found to sometimes be poor. Such a result could be used to aid a stratigrapher in rethinking or questioning a proposed correlation. This rethinking might not happen without the input from the intelligent system.

The quality of online antidepressant drug information: an evaluation of English and Finnish language Web sites.

PubMed

Prusti, Marjo; Lehtineva, Susanna; Pohjanoksa-Mäntylä, Marika; Bell, J Simon

2012-01-01

The Internet is a frequently used source of drug information, including among people with mental disorders. Online drug information may be narrow in scope, incomplete, and contain errors of omission. To evaluate the quality of online antidepressant drug information in English and Finnish. Forty Web sites were identified using the search terms antidepressants and masennuslääkkeet in English and Finnish, respectively. Included Web sites (14 English, 8 Finnish) were evaluated for aesthetics, interactivity, content coverage, and content correctness using published criteria. All Web sites were assessed using the Date, Author, References, Type, Sponsor (DARTS) and DISCERN quality assessment tools. English and Finnish Web sites had similar aesthetics, content coverage, and content correctness scores. English Web sites were more interactive than Finnish Web sites (P<.05). Overall, adverse drug reactions were covered on 21 of 22 Web sites; however, drug-alcohol interactions were addressed on only 9 of 22 Web sites, and dose was addressed on only 6 of 22 Web sites. Few (2/22 Web sites) provided incorrect information. The DISCERN score was significantly correlated with content coverage (r=0.670, P<.01), content correctness (r=0.663, P<.01), and the DARTS score (r=0.459, P<.05). No Web site provided information about all aspects of antidepressant treatment. Nevertheless, few Web sites provided incorrect information. Both English and Finnish Web sites were similar in terms of aesthetics, content coverage, and content correctness. Copyright © 2012 Elsevier Inc. All rights reserved.

Meeting Reference Responsibilities through Library Web Sites.

ERIC Educational Resources Information Center

Adams, Michael

2001-01-01

Discusses library Web sites and explains some of the benefits when libraries make their sites into reference portals, linking them to other useful Web sites. Topics include print versus Web information sources; limitations of search engines; what Web sites to include, including criteria for inclusions; and organizing the sites. (LRW)

BLOODR: blood donor and requester mobile application

PubMed Central

Tatikonda, Vamsi Krishna

2017-01-01

Background With rapid increase in the usage of social networks sites across the world, there is also a steady increase in blood donation requests as being noticed in the number of posts on these sites such as Facebook and twitter seeking blood donors. Finding blood donor is a challenging issue in almost every country. There are some blood donor finder applications in the market such as Blood app by Red Cross and Blood Donor Finder application by Neologix. However, more reliable applications that meet the needs of users are prompted. Methods Several software technologies including languages and framework are used to develop our blood-donor web application known as BLOODR application. These technologies comprise Ruby programming language (simply known as Ruby) along with JavaScript and PostgreSQL for database are used. Ruby on Rails (simply known as Rails) is an open source Web framework that makes it possible to quickly and easily create data-based web applications. Results We show screenshots for the BLOODR application for different types of users including requester, donor, and administrator. Various features of the application are described and their needs of use are analyzed. If a patient needs a blood at a clinic, blood donors in vicinity can be contacted through using a clinic management service provided in this application. Registered donors will get notification for the blood requests only if their blood group is compatible with the requested blood type and in the same city/region. Then matching blood donors can go to the requesting clinic and donate. Conclusions BLOODR application provides a reliable platform to connect local blood donors with patients. BLOODR creates a communication channel through authenticated clinics whenever a patient needs blood donation. It is a useful tool to find compatible blood donors who can receive blood request posts in their local area. Clinics can use this web application to maintain the blood donation activity. Future improvement of the BLOODR is explained. PMID:29184892

BLOODR: blood donor and requester mobile application.

PubMed

Tatikonda, Vamsi Krishna; El-Ocla, Hosam

2017-01-01

With rapid increase in the usage of social networks sites across the world, there is also a steady increase in blood donation requests as being noticed in the number of posts on these sites such as Facebook and twitter seeking blood donors. Finding blood donor is a challenging issue in almost every country. There are some blood donor finder applications in the market such as Blood app by Red Cross and Blood Donor Finder application by Neologix. However, more reliable applications that meet the needs of users are prompted. Several software technologies including languages and framework are used to develop our blood-donor web application known as BLOODR application. These technologies comprise Ruby programming language (simply known as Ruby) along with JavaScript and PostgreSQL for database are used. Ruby on Rails (simply known as Rails) is an open source Web framework that makes it possible to quickly and easily create data-based web applications. We show screenshots for the BLOODR application for different types of users including requester, donor, and administrator. Various features of the application are described and their needs of use are analyzed. If a patient needs a blood at a clinic, blood donors in vicinity can be contacted through using a clinic management service provided in this application. Registered donors will get notification for the blood requests only if their blood group is compatible with the requested blood type and in the same city/region. Then matching blood donors can go to the requesting clinic and donate. BLOODR application provides a reliable platform to connect local blood donors with patients. BLOODR creates a communication channel through authenticated clinics whenever a patient needs blood donation. It is a useful tool to find compatible blood donors who can receive blood request posts in their local area. Clinics can use this web application to maintain the blood donation activity. Future improvement of the BLOODR is explained.

[A systematic evaluation of application of the web-based cancer database].

PubMed

Huang, Tingting; Liu, Jialin; Li, Yong; Zhang, Rui

2013-10-01

In order to support the theory and practice of the web-based cancer database development in China, we applied a systematic evaluation to assess the development condition of the web-based cancer databases at home and abroad. We performed computer-based retrieval of the Ovid-MEDLINE, Springerlink, EBSCOhost, Wiley Online Library and CNKI databases, the papers of which were published between Jan. 1995 and Dec. 2011, and retrieved the references of these papers by hand. We selected qualified papers according to the pre-established inclusion and exclusion criteria, and carried out information extraction and analysis of the papers. Eventually, searching the online database, we obtained 1244 papers, and checking the reference lists, we found other 19 articles. Thirty-one articles met the inclusion and exclusion criteria and we extracted the proofs and assessed them. Analyzing these evidences showed that the U.S.A. counted for 26% in the first place. Thirty-nine percent of these web-based cancer databases are comprehensive cancer databases. As for single cancer databases, breast cancer and prostatic cancer are on the top, both counting for 10% respectively. Thirty-two percent of the cancer database are associated with cancer gene information. For the technical applications, MySQL and PHP applied most widely, nearly 23% each.

A new web-based system to improve the monitoring of snow avalanche hazard in France

NASA Astrophysics Data System (ADS)

Bourova, Ekaterina; Maldonado, Eric; Leroy, Jean-Baptiste; Alouani, Rachid; Eckert, Nicolas; Bonnefoy-Demongeot, Mylene; Deschatres, Michael

2016-05-01

Snow avalanche data in the French Alps and Pyrenees have been recorded for more than 100 years in several databases. The increasing amount of observed data required a more integrative and automated service. Here we report the comprehensive web-based Snow Avalanche Information System newly developed to this end for three important data sets: an avalanche chronicle (Enquête Permanente sur les Avalanches, EPA), an avalanche map (Carte de Localisation des Phénomènes d'Avalanche, CLPA) and a compilation of hazard and vulnerability data recorded on selected paths endangering human settlements (Sites Habités Sensibles aux Avalanches, SSA). These data sets are now integrated into a common database, enabling full interoperability between all different types of snow avalanche records: digitized geographic data, avalanche descriptive parameters, eyewitness reports, photographs, hazard and risk levels, etc. The new information system is implemented through modular components using Java-based web technologies with Spring and Hibernate frameworks. It automates the manual data entry and improves the process of information collection and sharing, enhancing user experience and data quality, and offering new outlooks to explore and exploit the huge amount of snow avalanche data available for fundamental research and more applied risk assessment.

Status Report for Remediation Decision Support Project, Task 1, Activity 1.B – Physical and Hydraulic Properties Database and Interpretation

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

Rockhold, Mark L.

2008-09-26

The objective of Activity 1.B of the Remediation Decision Support (RDS) Project is to compile all available physical and hydraulic property data for sediments from the Hanford Site, to port these data into the Hanford Environmental Information System (HEIS), and to make the data web-accessible to anyone on the Hanford Local Area Network via the so-called Virtual Library. In past years efforts were made by RDS project staff to compile all available physical and hydraulic property data for Hanford sediments and to transfer these data into SoilVision{reg_sign}, a commercial geotechnical software package designed for storing, analyzing, and manipulating soils data.more » Although SoilVision{reg_sign} has proven to be useful, its access and use restrictions have been recognized as a limitation to the effective use of the physical and hydraulic property databases by the broader group of potential users involved in Hanford waste site issues. In order to make these data more widely available and useable, a decision was made to port them to HEIS and to make them web-accessible via a Virtual Library module. In FY08 the objectives of Activity 1.B of the RDS Project were to: (1) ensure traceability and defensibility of all physical and hydraulic property data currently residing in the SoilVision{reg_sign} database maintained by PNNL, (2) transfer the physical and hydraulic property data from the Microsoft Access database files used by SoilVision{reg_sign} into HEIS, which has most recently been maintained by Fluor-Hanford, Inc., (3) develop a Virtual Library module for accessing these data from HEIS, and (4) write a User's Manual for the Virtual Library module. The development of the Virtual Library module was to be performed by a third party under subcontract to Fluor. The intent of these activities is to make the available physical and hydraulic property data more readily accessible and useable by technical staff and operable unit managers involved in waste site assessments and remedial action decisions for Hanford. This status report describes the history of this development effort and progress to date.« less

Benefits of a comprehensive quality program for cryopreserved PBMC covering 28 clinical trials sites utilizing an integrated, analytical web-based portal.

PubMed

Ducar, Constance; Smith, Donna; Pinzon, Cris; Stirewalt, Michael; Cooper, Cristine; McElrath, M Juliana; Hural, John

2014-07-01

The HIV Vaccine Trials Network (HVTN) is a global network of 28 clinical trial sites dedicated to identifying an effective HIV vaccine. Cryopreservation of high-quality peripheral blood mononuclear cells (PBMC) is critical for the assessment of vaccine-induced cellular immune functions. The HVTN PBMC Quality Management Program is designed to ensure that viable PBMC are processed, stored and shipped for clinical trial assays from all HVTN clinical trial sites. The program has evolved by developing and incorporating best practices for laboratory and specimen quality and implementing automated, web-based tools. These tools allow the site-affiliated processing laboratories and the central Laboratory Operations Unit to rapidly collect, analyze and report PBMC quality data. The HVTN PBMC Quality Management Program includes five key components: 1) Laboratory Assessment, 2) PBMC Training and Certification, 3) Internal Quality Control, 4) External Quality Control (EQC), and 5) Assay Specimen Quality Control. Fresh PBMC processing data is uploaded from each clinical site processing laboratory to a central HVTN Statistical and Data Management Center database for access and analysis on a web portal. Samples are thawed at a central laboratory for assay or specimen quality control and sample quality data is uploaded directly to the database by the central laboratory. Four year cumulative data covering 23,477 blood draws reveals an average fresh PBMC yield of 1.45×10(6)±0.48 cells per milliliter of useable whole blood. 95% of samples were within the acceptable range for fresh cell yield of 0.8-3.2×10(6) cells/ml of usable blood. Prior to full implementation of the HVTN PBMC Quality Management Program, the 2007 EQC evaluations from 10 international sites showed a mean day 2 thawed viability of 83.1% and a recovery of 67.5%. Since then, four year cumulative data covering 3338 specimens used in immunologic assays shows that 99.88% had acceptable viabilities (>66%) for use in cellular assays (mean, 91.46% ±4.5%), and 96.2% had acceptable recoveries (50%-130%) with a mean of recovery of 85.8% ±19.12% of the originally cryopreserved cells. EQC testing revealed that since August 2009, failed recoveries dropped from 4.1% to 1.6% and failed viabilities dropped from 1.0% to 0.3%. The HVTN PBMC quality program provides for laboratory assessment, training and tools for identifying problems, implementing corrective action and monitoring for improvements. These data support the benefits of implementing a comprehensive, web-based PBMC quality program for large clinical trials networks. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of web tools to disseminate space geodesy data-related products

NASA Astrophysics Data System (ADS)

Soudarin, L.; Ferrage, P.; Mezerette, A.

2014-12-01

In order to promote the products of the DORIS system, the French Space Agency CNES has developed and implemented on the web site of the International DORIS Service (IDS) a set of plot tools to interactively build and display time series of site positions, orbit residuals and terrestrial parameters (scale, geocenter). An interactive global map is also available to select sites, and to get access to their information. Besides the products provided by the CNES Orbitography Team and the IDS components, these tools allow comparing time evolutions of coordinates for collocated DORIS and GNSS stations, thanks to the collaboration with the Terrestrial Frame Combination Center of the International GNSS Service (IGS). The next step currently in progress is the creation of a database to improve robustness and efficiency of the tools, with the objective to propose a complete web service to foster data exchange with the other geodetic services of the International Association of Geodesy (IAG). The possibility to visualize and compare position time series of the four main space geodetic techniques DORIS, GNSS, SLR and VLBI is already under way at the French level. A dedicated version of these web tools has been developed for the French Space Geodesy Research Group (GRGS). It will give access to position time series provided by the GRGS Analysis Centers involved in DORIS, GNSS, SLR and VLBI data processing for the realization of the International Terrestrial Reference Frame. In this presentation, we will describe the functionalities of these tools, and we will address some aspects of the time series (content, format).

A simple method for serving Web hypermaps with dynamic database drill-down

PubMed Central

Boulos, Maged N Kamel; Roudsari, Abdul V; Carson, Ewart R

2002-01-01

Background HealthCyberMap aims at mapping parts of health information cyberspace in novel ways to deliver a semantically superior user experience. This is achieved through "intelligent" categorisation and interactive hypermedia visualisation of health resources using metadata, clinical codes and GIS. HealthCyberMap is an ArcView 3.1 project. WebView, the Internet extension to ArcView, publishes HealthCyberMap ArcView Views as Web client-side imagemaps. The basic WebView set-up does not support any GIS database connection, and published Web maps become disconnected from the original project. A dedicated Internet map server would be the best way to serve HealthCyberMap database-driven interactive Web maps, but is an expensive and complex solution to acquire, run and maintain. This paper describes HealthCyberMap simple, low-cost method for "patching" WebView to serve hypermaps with dynamic database drill-down functionality on the Web. Results The proposed solution is currently used for publishing HealthCyberMap GIS-generated navigational information maps on the Web while maintaining their links with the underlying resource metadata base. Conclusion The authors believe their map serving approach as adopted in HealthCyberMap has been very successful, especially in cases when only map attribute data change without a corresponding effect on map appearance. It should be also possible to use the same solution to publish other interactive GIS-driven maps on the Web, e.g., maps of real world health problems. PMID:12437788

Accessibility and content of individualized adult reconstructive hip and knee/musculoskeletal oncology fellowship web sites.

PubMed

Young, Bradley L; Cantrell, Colin K; Patt, Joshua C; Ponce, Brent A

2018-06-01

Accessible, adequate online information is important to fellowship applicants. Program web sites can affect which programs applicants apply to, subsequently altering interview costs incurred by both parties and ultimately impacting rank lists. Web site analyses have been performed for all orthopaedic subspecialties other than those involved in the combined adult reconstruction and musculoskeletal (MSK) oncology fellowship match. A complete list of active programs was obtained from the official adult reconstruction and MSK oncology society web sites. Web site accessibility was assessed using a structured Google search. Accessible web sites were evaluated based on 21 previously reported content criteria. Seventy-four adult reconstruction programs and 11 MSK oncology programs were listed on the official society web sites. Web sites were identified and accessible for 58 (78%) adult reconstruction and 9 (82%) MSK oncology fellowship programs. No web site contained all content criteria and more than half of both adult reconstruction and MSK oncology web sites failed to include 12 of the 21 criteria. Several programs participating in the combined Adult Reconstructive Hip and Knee/Musculoskeletal Oncology Fellowship Match did not have accessible web sites. Of the web sites that were accessible, none contained comprehensive information and the majority lacked information that has been previously identified as being important to perspective applicants.

A systematic review of patient inflammatory bowel disease information resources on the World Wide Web.

PubMed

Bernard, André; Langille, Morgan; Hughes, Stephanie; Rose, Caren; Leddin, Desmond; Veldhuyzen van Zanten, Sander

2007-09-01

The Internet is a widely used information resource for patients with inflammatory bowel disease, but there is variation in the quality of Web sites that have patient information regarding Crohn's disease and ulcerative colitis. The purpose of the current study is to systematically evaluate the quality of these Web sites. The top 50 Web sites appearing in Google using the terms "Crohn's disease" or "ulcerative colitis" were included in the study. Web sites were evaluated using a (a) Quality Evaluation Instrument (QEI) that awarded Web sites points (0-107) for specific information on various aspects of inflammatory bowel disease, (b) a five-point Global Quality Score (GQS), (c) two reading grade level scores, and (d) a six-point integrity score. Thirty-four Web sites met the inclusion criteria, 16 Web sites were excluded because they were portals or non-IBD oriented. The median QEI score was 57 with five Web sites scoring higher than 75 points. The median Global Quality Score was 2.0 with five Web sites achieving scores of 4 or 5. The average reading grade level score was 11.2. The median integrity score was 3.0. There is marked variation in the quality of the Web sites containing information on Crohn's disease and ulcerative colitis. Many Web sites suffered from poor quality but there were five high-scoring Web sites.

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

Lysine acetylation sites prediction using an ensemble of support vector machine classifiers.

PubMed

Xu, Yan; Wang, Xiao-Bo; Ding, Jun; Wu, Ling-Yun; Deng, Nai-Yang

2010-05-07

Lysine acetylation is an essentially reversible and high regulated post-translational modification which regulates diverse protein properties. Experimental identification of acetylation sites is laborious and expensive. Hence, there is significant interest in the development of computational methods for reliable prediction of acetylation sites from amino acid sequences. In this paper we use an ensemble of support vector machine classifiers to perform this work. The experimentally determined acetylation lysine sites are extracted from Swiss-Prot database and scientific literatures. Experiment results show that an ensemble of support vector machine classifiers outperforms single support vector machine classifier and other computational methods such as PAIL and LysAcet on the problem of predicting acetylation lysine sites. The resulting method has been implemented in EnsemblePail, a web server for lysine acetylation sites prediction available at http://www.aporc.org/EnsemblePail/. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

SNPversity: a web-based tool for visualizing diversity

PubMed Central

Schott, David A; Vinnakota, Abhinav G; Portwood, John L; Andorf, Carson M

2018-01-01

Abstract Many stand-alone desktop software suites exist to visualize single nucleotide polymorphism (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualization tool that can be implemented on a Unix-like machine and served through a web browser that can be accessible worldwide. SNPversity consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. SNPversity displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state. SNPversity is currently available at MaizeGDB, the maize community’s database, and will be soon available at GrainGenes, the clade-oriented database for Triticeae and Avena species, including wheat, barley, rye, and oat. The code and documentation are uploaded onto github, and they are freely available to the public. We expect that the tool will be highly useful for other biological databases with a similar need to display SNP diversity through their web interfaces. Database URL: https://www.maizegdb.org/snpversity PMID:29688387

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.

PubMed

Attimonelli, Marcella; Catalano, Domenico; Gissi, Carmela; Grillo, Giorgio; Licciulli, Flavio; Liuni, Sabino; Santamaria, Monica; Pesole, Graziano; Saccone, Cecilia

2002-01-01

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organelle genomes. Mitochondrial genomes have been extensively sequenced and analysed and data have been collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc, a database containing detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa. The MitoNuc database can be retrieved through SRS and is available via the web site http://bighost.area.ba.cnr.it/mitochondriome where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, links to other mitochondrial sites and related information, are available. The MitoAln database, related to MitoNuc in the previous release, reporting the multiple alignments of the relevant homologous protein coding regions, is no longer supported in the present release. In order to keep the links among entries in MitoNuc from homologous proteins, a new field in the database has been defined: the cluster identifier, an alpha numeric code used to identify each cluster of homologous proteins. A comment field derived from the corresponding SWISS-PROT entry has been introduced; this reports clinical data related to dysfunction of the protein. The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented.

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

Golfing with protons: using research grade simulation algorithms for online games

NASA Astrophysics Data System (ADS)

Harold, J.

2004-12-01

Scientists have long known the power of simulations. By modeling a system in a computer, researchers can experiment at will, developing an intuitive sense of how a system behaves. The rapid increase in the power of personal computers, combined with technologies such as Flash, Shockwave and Java, allow us to bring research simulations into the education world by creating exploratory environments for the public. This approach is illustrated by a project funded by a small grant from NSF's Informal Science Education program, through an opportunity that provides education supplements to existing research awards. Using techniques adapted from a magnetospheric research program, several Flash based interactives have been developed that allow web site visitors to explore the motion of particles in the Earth's magnetosphere. These pieces were folded into a larger Space Weather Center web project at the Space Science Institute (www.spaceweathercenter.org). Rather than presenting these interactives as plasma simulations per se, the research algorithms were used to create games such as "Magneto Mini Golf", where the balls are protons moving in combined electric and magnetic fields. The "holes" increase in complexity, beginning with no fields and progressing towards a simple model of Earth's magnetosphere. The emphasis of the activity is gameplay, but because it is at its core a plasma simulation, the user develops an intuitive sense of charged particle motion as they progress. Meanwhile, the pieces contain embedded assessments that are measurable through a database driven tracking system. Mining that database not only provides helpful usability information, but allows us to examine whether users are meeting the learning goals of the activities. We will discuss the development and evaluation results of the project, as well as the potential for these types of activities to shift the expectations of what a web site can and should provide educationally.

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

Reservoir High's TE Site Wins Web Site of the Month

ERIC Educational Resources Information Center

Tech Directions, 2008

2008-01-01

This article features "Mr. Rhine's Technology Education Web Site," a winner of the Web Site of the Month. This Web site was designed by Luke Rhine, a teacher at the Reservoir High School in Fulton, Maryland. Rhine's Web site offers course descriptions and syllabuses, class calendars, lectures and presentations, design briefs and other course…

The Way of the Web: Answers to Your Questions about Web Site Marketing.

ERIC Educational Resources Information Center

Wassom, Julie

2002-01-01

Provides suggestions for effective web site marketing for child care and early education programs. Includes key considerations in designing a web site, specific elements that cause visitors to stay on and return to the site, use of interactive sites, web-site updating and revision, and use of traditional marketing activities to direct prospective…

Automated CFD Database Generation for a 2nd Generation Glide-Back-Booster

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.; Rogers, Stuart E.; Aftosmis, Michael J.; Pandya, Shishir A.; Ahmad, Jasim U.; Tejmil, Edward

2003-01-01

A new software tool, AeroDB, is used to compute thousands of Euler and Navier-Stokes solutions for a 2nd generation glide-back booster in one week. The solution process exploits a common job-submission grid environment using 13 computers located at 4 different geographical sites. Process automation and web-based access to the database greatly reduces the user workload, removing much of the tedium and tendency for user input errors. The database consists of forces, moments, and solution files obtained by varying the Mach number, angle of attack, and sideslip angle. The forces and moments compare well with experimental data. Stability derivatives are also computed using a monotone cubic spline procedure. Flow visualization and three-dimensional surface plots are used to interpret and characterize the nature of computed flow fields.

Database support for adaptation to climate change: An assessment of web-based portals across scales.

PubMed

Sanderson, Hans; Hilden, Mikael; Russel, Duncan; Dessai, Suraje

2016-10-01

The widely recognized increase in greenhouse gas emissions is necessitating adaptation to a changing climate, and policies are being developed and implemented worldwide, across sectors, and between government scales globally. The aim of this article is to reflect on one of the major challenges: facilitating and sharing information on the next adaptation practices. Web portals (i.e., web sites) for disseminating information are important tools in meeting this challenge, and therefore, we assessed the characteristics of select major portals across multiple scales. We found that there is a rather limited number of case studies available in the portals-between 900 and 1000 in total-with 95 that include cost information and 195 that include the participation of stakeholders globally. Portals are rarely cited by researchers, suggesting a suboptimal connection between the practical, policy-related, and scientific development of adaptation. The government portals often lack links on search results between US and European Union (EU) web sites, for example. With significant investments and policy development emerging in both the United States and the European Union, there is great potential to share information via portals. Moreover, there is the possibility of better connecting the practical adaptation experience from bottom-up projects to the science of adaptation. Integr Environ Assess Manag 2016;12:627-631. © 2016 SETAC. © 2016 SETAC.

Web Site Credibility: Why Do People Believe What They Believe?

ERIC Educational Resources Information Center

Iding, Marie K.; Crosby, Martha E.; Auernheimer, Brent; Klemm, E. Barbara

2009-01-01

This research investigates university students' determinations of credibility of information on Web sites, confidence in their determinations, and perceptions of Web site authors' vested interests. In Study 1, university-level computer science and education students selected Web sites determined to be credible and Web sites that exemplified…

Personality in cyberspace: personal Web sites as media for personality expressions and impressions.

PubMed

Marcus, Bernd; Machilek, Franz; Schütz, Astrid

2006-06-01

This research examined the personality of owners of personal Web sites based on self-reports, visitors' ratings, and the content of the Web sites. The authors compared a large sample of Web site owners with population-wide samples on the Big Five dimensions of personality. Controlling for demographic differences, the average Web site owner reported being slightly less extraverted and more open to experience. Compared with various other samples, Web site owners did not generally differ on narcissism, self-monitoring, or self-esteem, but gender differences on these traits were often smaller in Web site owners. Self-other agreement was highest with Openness to Experience, but valid judgments of all Big Five dimensions were derived from Web sites providing rich information. Visitors made use of quantifiable features of the Web site to infer personality, and the cues they utilized partly corresponded to self-reported traits. Copyright 2006 APA, all rights reserved.

Digital Earth Watch (DEW): How Mobile Apps Are Paving The Way Towards A Federated Web-Services Architecture For Citizen Science

NASA Astrophysics Data System (ADS)

Carrera, F.; Schloss, A. L.; Guerin, S.; Beaudry, J.; Pickle, J.

2011-12-01

Dozens of web-based initiatives allow citizens to provide information to programs that monitor the health of our environment. A concerned citizen can participate on-line as a weather "spotter", provide important phenological information to national databases, update bird counts in the area, or record the freezing of ponds, and much more. Many of these programs are developing mobile apps as companion tools to their web sites. Our group was involved in the development of one such companion app as an adjunct to the Picture Post project web site. Digital Earth Watch (DEW) and the Picture Post network support environmental monitoring through repeat digital photography and satellite imagery. A Picture Post is an eight-sided platform on a stand-alone post for taking a panoramic series of photographs. By taking pictures on a regular basis at Picture Post sites and by sharing these pictures on the program's web site (housed at the University of New Hampshire), citizen scientists are creating a photographic library of change-over-time in their local area and contributing to national monitoring programs. Our DEW Android application simplifies participation by allowing users to upload pictures instantly from their smart phone. The app also removes the constraint of the physical picture post, by allowing users to create a virtual post anywhere in the world. Posts have been set up to monitor trails, forests, water, wetlands, gardens and landscapes. The app uses the phone's GPS to position the virtual post in its geographic location and guides the user through the orientations thanks to the internal accelerometers and compass. To aid in the before-and-after comparison of images taken from the same orientation, the DEW app displays an "onionskin" of the prior image overlayed onto the camera viewfinder. With the transparent onionskin as a guide, the user can align the images more accurately, thus allowing differences between pictures to be detectable and measurable. The app interacts with the UNH server via APIs (Application Programming Interfaces) that were created to allow bi-directional machine-to-machine interaction between the mobile device and the web site. Thus, the principal functions that a user can perform on the web site, such as finding post sites on a map and viewing and adding picture sets, are available on the smartphone. The development of the APIs makes it now possible not only to communicate with our own mobile app, but, more importantly, it opens the door for other computer systems to directly interact with our server. Our ongoing discussions with the National Phenology Network and Project Budburst, have highlighted the potential (and perhaps the need) for the creation of a distributed web-service architecture whereby each national program exposes its key functionalities not only to their own mobile phone apps, but also to other organizations, in a federated system of servers, all supporting citizen-based digital earth watch programs.

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

XCOM: Photon Cross Sections Database

National Institute of Standards and Technology Data Gateway

SRD 8 XCOM: Photon Cross Sections Database (Web, free access)   A web database is provided which can be used to calculate photon cross sections for scattering, photoelectric absorption and pair production, as well as total attenuation coefficients, for any element, compound or mixture (Z <= 100) at energies from 1 keV to 100 GeV.

A Fully Automated Method of Locating Building Shadows for Aerosol Optical Depth Calculations in High-Resolution Satellite Imagery

DTIC Science & Technology

2010-09-01

absorption, limiting the effectiveness of intelligence collection and weapon systems that operate in those portions of the spectrum by reducing the amount of... Intelligence Agency Web site in NITF 2.0 format. This study used basic imagery from DigitalGlobe (QuickBird, WorldView-1). This imagery is not...databases. Militarily, FASTEC could enable in-scene correction in intelligence collection and possibly influence electro- optical targeting decisions

Kangaroo – A pattern-matching program for biological sequences

PubMed Central

2002-01-01

Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718

WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

PubMed Central

Wangkumhang, Pongsakorn; Chaichoompu, Kridsadakorn; Ngamphiw, Chumpol; Ruangrit, Uttapong; Chanprasert, Juntima; Assawamakin, Anunchai; Tongsima, Sissades

2007-01-01

Background Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. Results This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. Conclusion WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at . PMID:17697334

Sequence-Based Prediction of RNA-Binding Residues in Proteins.

PubMed

Walia, Rasna R; El-Manzalawy, Yasser; Honavar, Vasant G; Dobbs, Drena

2017-01-01

Identifying individual residues in the interfaces of protein-RNA complexes is important for understanding the molecular determinants of protein-RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein-RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein-RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods that can reliably identify interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA partner.

Sequence-Based Prediction of RNA-Binding Residues in Proteins

PubMed Central

Walia, Rasna R.; EL-Manzalawy, Yasser; Honavar, Vasant G.; Dobbs, Drena

2017-01-01

Identifying individual residues in the interfaces of protein–RNA complexes is important for understanding the molecular determinants of protein–RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein–RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein–RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods that can reliably identify interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA partner. PMID:27787829

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

Perceptions of Business Students' Feature Requirements in Educational Web Sites

ERIC Educational Resources Information Center

Hazari, Sunil; Johnson, Barbara

2007-01-01

There is paucity of original research that explains phenomena related to content organization and site design of educational Web sites. Educational Web sites are often used to provide Web-based instruction, which itself is a relatively recent phenomenon for business schools, and additional research is needed in this area. Educational Web sites are…

JAMSTEC E-library of Deep-sea Images (J-EDI) Realizes a Virtual Journey to the Earth's Unexplored Deep Ocean

NASA Astrophysics Data System (ADS)

Sasaki, T.; Azuma, S.; Matsuda, S.; Nagayama, A.; Ogido, M.; Saito, H.; Hanafusa, Y.

2016-12-01

The Japan Agency for Marine-Earth Science and Technology (JAMSTEC) archives a large amount of deep-sea research videos and photos obtained by JAMSTEC's research submersibles and vehicles with cameras. The web site "JAMSTEC E-library of Deep-sea Images : J-EDI" (http://www.godac.jamstec.go.jp/jedi/e/) has made videos and photos available to the public via the Internet since 2011. Users can search for target videos and photos by keywords, easy-to-understand icons, and dive information at J-EDI because operating staffs classify videos and photos as to contents, e.g. living organism and geological environment, and add comments to them.Dive survey data including videos and photos are not only valiant academically but also helpful for education and outreach activities. With the aim of the improvement of visibility for broader communities, we added new functions of 3-dimensional display synchronized various dive survey data with videos in this year.New Functions Users can search for dive survey data by 3D maps with plotted dive points using the WebGL virtual map engine "Cesium". By selecting a dive point, users can watch deep-sea videos and photos and associated environmental data, e.g. water temperature, salinity, rock and biological sample photos, obtained by the dive survey. Users can browse a dive track visualized in 3D virtual spaces using the WebGL JavaScript library. By synchronizing this virtual dive track with videos, users can watch deep-sea videos recorded at a point on a dive track. Users can play an animation which a submersible-shaped polygon automatically traces a 3D virtual dive track and displays of dive survey data are synchronized with tracing a dive track. Users can directly refer to additional information of other JAMSTEC data sites such as marine biodiversity database, marine biological sample database, rock sample database, and cruise and dive information database, on each page which a 3D virtual dive track is displayed. A 3D visualization of a dive track makes users experience a virtual dive survey. In addition, by synchronizing a virtual dive track with videos, it is easy to understand living organisms and geological environments of a dive point. Therefore, these functions will visually support understanding of deep-sea environments in lectures and educational activities.

Web site development: applying aesthetics to promote breast health education and awareness.

PubMed

Thomas, Barbara; Goldsmith, Susan B; Forrest, Anne; Marshall, Renée

2002-01-01

This article describes the process of establishing a Web site as part of a collaborative project using visual art to promote breast health education. The need for a more "user-friendly" comprehensive breast health Web site that is aesthetically rewarding was identified after an analysis of current Web sites available through the World Wide Web. Two predetermined sets of criteria, accountability and aesthetics, were used to analyze these sites and to generate ideas for creating a breast health education Web site using visual art. Results of the analyses conducted are included as well as the factors to consider for incorporating into a Web site. The process specified is thorough and can be applied to establish a Web site that is aesthetically rewarding and informative for a variety of educational purposes.

The INGV Real Time Strong Motion Database

NASA Astrophysics Data System (ADS)

Massa, Marco; D'Alema, Ezio; Mascandola, Claudia; Lovati, Sara; Scafidi, Davide; Gomez, Antonio; Carannante, Simona; Franceschina, Gianlorenzo; Mirenna, Santi; Augliera, Paolo

2017-04-01

The INGV real time strong motion data sharing is assured by the INGV Strong Motion Database. ISMD (http://ismd.mi.ingv.it) was designed in the last months of 2011 in cooperation among different INGV departments, with the aim to organize the distribution of the INGV strong-motion data using standard procedures for data acquisition and processing. The first version of the web portal was published soon after the occurrence of the 2012 Emilia (Northern Italy), Mw 6.1, seismic sequence. At that time ISMD was the first European real time web portal devoted to the engineering seismology community. After four years of successfully operation, the thousands of accelerometric waveforms collected in the archive need necessary a technological improvement of the system in order to better organize the new data archiving and to make more efficient the answer to the user requests. ISMD 2.0 was based on PostgreSQL (www.postgresql.org), an open source object- relational database. The main purpose of the web portal is to distribute few minutes after the origin time the accelerometric waveforms and related metadata of the Italian earthquakes with ML≥3.0. Data are provided both in raw SAC (counts) and automatically corrected ASCII (gal) formats. The web portal also provide, for each event, a detailed description of the ground motion parameters (i.e. Peak Ground Acceleration, Velocity and Displacement, Arias and Housner Intensities) data converted in velocity and displacement, response spectra up to 10.0 s and general maps concerning the recent and the historical seismicity of the area together with information about its seismic hazard. The focal parameters of the events are provided by the INGV National Earthquake Center (CNT, http://cnt.rm.ingv.it). Moreover, the database provides a detailed site characterization section for each strong motion station, based on geological, geomorphological and geophysical information. At present (i.e. January 2017), ISMD includes 987 (121.185 waveforms) Italian earthquakes with ML≥3.0, recorded since the 1st January 2012, besides 204 accelerometric stations belonging to the INGV strong motion network and regional partner.

Photosynthesis and the web: 2001.

PubMed

Orr, L

2001-01-01

First, a brief history of the Internet and the World Wide Web is presented. This is followed by relevant information on photosynthesis-related web sites grouped into several categories: (1) large group sites, (2) comprehensive overview sites, (3) specific subject sites, (4) individual researcher sites, (5) kindergarten through high school (K-12) educational sites, (6) books and journals, and, 7) other useful sites. A section on searching the Web is also included. Finally, we have included an appendix with all of the web sites discussed herein as well as other web sites that space did not allow. Readers are requested to send comments, corrections and additions to gov@uiuc.edu.

How Japanese students characterize information from web-sites.

PubMed

Iwahara, A; Yamada, M; Hatta, T; Kawakami, A; Okamoto, M

2000-12-01

How 352 Japanese university students regard web-site information was investigated by two kinds of survey. Application of correspondence analysis and cluster analysis to the questionnaire responses to the web-site advertisement showed students regarded a web-site as a new alien medium which is different from current media. Students regarded web-sites as simply complicated, intellectual, and impermanent, or not memorable. Students got precise information from web-sites but they did not use it in making decisions to purchase goods.

Design of a Web-tool for diagnostic clinical trials handling medical imaging research.

PubMed

Baltasar Sánchez, Alicia; González-Sistal, Angel

2011-04-01

New clinical studies in medicine are based on patients and controls using different imaging diagnostic modalities. Medical information systems are not designed for clinical trials employing clinical imaging. Although commercial software and communication systems focus on storage of image data, they are not suitable for storage and mining of new types of quantitative data. We sought to design a Web-tool to support diagnostic clinical trials involving different experts and hospitals or research centres. The image analysis of this project is based on skeletal X-ray imaging. It involves a computerised image method using quantitative analysis of regions of interest in healthy bone and skeletal metastases. The database is implemented with ASP.NET 3.5 and C# technologies for our Web-based application. For data storage, we chose MySQL v.5.0, one of the most popular open source databases. User logins were necessary, and access to patient data was logged for auditing. For security, all data transmissions were carried over encrypted connections. This Web-tool is available to users scattered at different locations; it allows an efficient organisation and storage of data (case report form) and images and allows each user to know precisely what his task is. The advantages of our Web-tool are as follows: (1) sustainability is guaranteed; (2) network locations for collection of data are secured; (3) all clinical information is stored together with the original images and the results derived from processed images and statistical analysis that enable us to perform retrospective studies; (4) changes are easily incorporated because of the modular architecture; and (5) assessment of trial data collected at different sites is centralised to reduce statistical variance.

Web sites for postpartum depression: convenient, frustrating, incomplete, and misleading.

PubMed

Summers, Audra L; Logsdon, M Cynthia

2005-01-01

To evaluate the content and the technology of Web sites providing information on postpartum depression. Eleven search engines were queried using the words "Postpartum Depression." The top 10 sites in each search engine were evaluated for correct content and technology using the Web Depression Tool, based on the Technology Assessment Model. Of the 36 unique Web sites located, 34 were available to review. Only five Web sites provided >75% correct responses to questions that summarized the current state of the science for postpartum depression. Eleven of the Web sites contained little or no useful information about postpartum depression, despite being among the first 10 Web sites listed by the search engine. Some Web sites contained possibly harmful suggestions for treatment of postpartum depression. In addition, there are many problems with the technology of Web sites providing information on postpartum depression. A better Web site for postpartum depression is necessary if we are to meet the needs of consumers for accurate and current information using technology that enhances learning. Since patient education is a core competency for nurses, it is essential that nurses understand how their patients are using the World Wide Web for learning and how we can assist our patients to find appropriate sites containing correct information.

An intelligent remote monitoring system for artificial heart.

PubMed

Choi, Jaesoon; Park, Jun W; Chung, Jinhan; Min, Byoung G

2005-12-01

A web-based database system for intelligent remote monitoring of an artificial heart has been developed. It is important for patients with an artificial heart implant to be discharged from the hospital after an appropriate stabilization period for better recovery and quality of life. Reliable continuous remote monitoring systems for these patients with life support devices are gaining practical meaning. The authors have developed a remote monitoring system for this purpose that consists of a portable/desktop monitoring terminal, a database for continuous recording of patient and device status, a web-based data access system with which clinicians can access real-time patient and device status data and past history data, and an intelligent diagnosis algorithm module that noninvasively estimates blood pump output and makes automatic classification of the device status. The system has been tested with data generation emulators installed on remote sites for simulation study, and in two cases of animal experiments conducted at remote facilities. The system showed acceptable functionality and reliability. The intelligence algorithm also showed acceptable practicality in an application to animal experiment data.

16 CFR 1130.8 - Requirements for Web site registration or alternative e-mail registration.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Requirements for Web site registration or... PRODUCTS (Eff. June 28, 2010) § 1130.8 Requirements for Web site registration or alternative e-mail registration. (a) Link to registration page. The manufacturer's Web site, or other Web site established for the...

22 CFR 502.6 - Terms of use for accessing program materials available on agency Web sites.

Code of Federal Regulations, 2014 CFR

2014-04-01

... available on agency Web sites. 502.6 Section 502.6 Foreign Relations BROADCASTING BOARD OF GOVERNORS... program materials available on agency Web sites. (a) By accessing Agency Web sites, Requestors agree to all the Terms of Use available on those Web sites. (b) All Requestors are advised that Agency program...

16 CFR 1130.8 - Requirements for Web site registration or alternative e-mail registration.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Requirements for Web site registration or... PRODUCTS § 1130.8 Requirements for Web site registration or alternative e-mail registration. (a) Link to registration page. The manufacturer's Web site, or other Web site established for the purpose of registration...

16 CFR 1130.8 - Requirements for Web site registration or alternative e-mail registration.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Requirements for Web site registration or... PRODUCTS § 1130.8 Requirements for Web site registration or alternative e-mail registration. (a) Link to registration page. The manufacturer's Web site, or other Web site established for the purpose of registration...

16 CFR 1130.7 - Requirements for Web site registration or alternative e-mail registration.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Requirements for Web site registration or... PRODUCTS § 1130.7 Requirements for Web site registration or alternative e-mail registration. (a) Link to registration page. The manufacturer's Web site, or other Web site established for the purpose of registration...

16 CFR § 1130.8 - Requirements for Web site registration or alternative e-mail registration.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Requirements for Web site registration or... OR TODDLER PRODUCTS § 1130.8 Requirements for Web site registration or alternative e-mail registration. (a) Link to registration page. The manufacturer's Web site, or other Web site established for the...

New design and facilities for the International Database for Absolute Gravity Measurements (AGrav): A support for the Establishment of a new Global Absolute Gravity Reference System

NASA Astrophysics Data System (ADS)

Wziontek, Hartmut; Falk, Reinhard; Bonvalot, Sylvain; Rülke, Axel

2017-04-01

After about 10 years of successful joint operation by BGI and BKG, the International Database for Absolute Gravity Measurements "AGrav" (see references hereafter) was under a major revision. The outdated web interface was replaced by a responsive, high level web application framework based on Python and built on top of Pyramid. Functionality was added, like interactive time series plots or a report generator and the interactive map-based station overview was updated completely, comprising now clustering and the classification of stations. Furthermore, the database backend was migrated to PostgreSQL for better support of the application framework and long-term availability. As comparisons of absolute gravimeters (AG) become essential to realize a precise and uniform gravity standard, the database was extended to document the results on international and regional level, including those performed at monitoring stations equipped with SGs. By this it will be possible to link different AGs and to trace their equivalence back to the key comparisons under the auspices of International Committee for Weights and Measures (CIPM) as the best metrological realization of the absolute gravity standard. In this way the new AGrav database accommodates the demands of the new Global Absolute Gravity Reference System as recommended by the IAG Resolution No. 2 adopted in Prague 2015. The new database will be presented with focus on the new user interface and new functionality, calling all institutions involved in absolute gravimetry to participate and contribute with their information to built up a most complete picture of high precision absolute gravimetry and improve its visibility. A Digital Object Identifier (DOI) will be provided by BGI to contributors to give a better traceability and facilitate the referencing of their gravity surveys. Links and references: BGI mirror site : http://bgi.obs-mip.fr/data-products/Gravity-Databases/Absolute-Gravity-data/ BKG mirror site: http://agrav.bkg.bund.de/agrav-meta/ Wilmes, H., H. Wziontek, R. Falk, S. Bonvalot (2009). AGrav - the New Absolute Gravity Database and a Proposed Cooperation with the GGP Project. J. of Geodynamics, 48, pp. 305-309. doi:10.1016/j.jog.2009.09.035. Wziontek, H., H. Wilmes, S. Bonvalot (2011). AGrav: An international database for absolute gravity measurements. In Geodesy for Planet Earth (S. Kenyon at al. eds). IAG Symposia, 136, 1035-1040, Springer, Berlin. 2011. doi:10.1007/978-3-642-20338-1_130.

Comparing Unique Title Coverage of Web of Science and Scopus in Earth and Atmospheric Sciences

ERIC Educational Resources Information Center

Barnett, Philip; Lascar, Claudia

2012-01-01

The current journal titles in earth and atmospheric sciences, that are unique to each of two databases, Web of Science and Scopus, were identified using different methods. Comparing by subject category shows that Scopus has hundreds of unique titles, and Web of Science just 16. The titles unique to each database have low SCImago Journal Rank…

Generic HTML Form Processor: A versatile PHP script to save web-collected data into a MySQL database.

PubMed

Göritz, Anja S; Birnbaum, Michael H

2005-11-01

The customizable PHP script Generic HTML Form Processor is intended to assist researchers and students in quickly setting up surveys and experiments that can be administered via the Web. This script relieves researchers from the burdens of writing new CGI scripts and building databases for each Web study. Generic HTML Form Processor processes any syntactically correct HTML forminput and saves it into a dynamically created open-source database. We describe five modes for usage of the script that allow increasing functionality but require increasing levels of knowledge of PHP and Web servers: The first two modes require no previous knowledge, and the fifth requires PHP programming expertise. Use of Generic HTML Form Processor is free for academic purposes, and its Web address is www.goeritz.net/brmic.

Turning Access into a web-enabled secure information system for clinical trials.

PubMed

Dongquan Chen; Chen, Wei-Bang; Soong, Mayhue; Soong, Seng-Jaw; Orthner, Helmuth F

2009-08-01

Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. We report a working procedure to transform and develop a standalone Access database into a secure Web-based secure information system. For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. The system lacks audit trails. The cost of development and maintenance may hinder its wide application. The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.

Characteristics of food industry web sites and "advergames" targeting children.

PubMed

Culp, Jennifer; Bell, Robert A; Cassady, Diana

2010-01-01

To assess the content of food industry Web sites targeting children by describing strategies used to prolong their visits and foster brand loyalty; and to document health-promoting messages on these Web sites. A content analysis was conducted of Web sites advertised on 2 children's networks, Cartoon Network and Nickelodeon. A total of 290 Web pages and 247 unique games on 19 Internet sites were examined. Games, found on 81% of Web sites, were the most predominant promotion strategy used. All games had at least 1 brand identifier, with logos being most frequently used. On average Web sites contained 1 "healthful" message for every 45 exposures to brand identifiers. Food companies use Web sites to extend their television advertising to promote brand loyalty among children. These sites almost exclusively promoted food items high in sugar and fat. Health professionals need to monitor food industry marketing practices used in "new media." Published by Elsevier Inc.

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.

PubMed

Chaudhuri, Rima; Sadrieh, Arash; Hoffman, Nolan J; Parker, Benjamin L; Humphrey, Sean J; Stöckli, Jacqueline; Hill, Adam P; James, David E; Yang, Jean Yee Hwa

2015-08-19

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus. PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

The effect of types of banner ad, Web localization, and customer involvement on Internet users' attitudes.

PubMed

Chen, Jengchung Victor; Ross, William H; Yen, David C; Akhapon, Lerdsuwankij

2009-02-01

In this study, three characteristics of Web sites were varied: types of banner ad, Web localization, and involvement in purchasing a product. The dependent variable was attitude toward the site. In laboratory experiments conducted in Thailand and Taiwan, participants browsed versions of a Web site containing different types of banner ads and products. As a within-participants factor, each participant browsed both a standardized English-language Web site and a localized Web site. Results showed that animated (rather than static) banner ads, localized versions (rather than a standardized version) of Web sites, and high (rather than low) product involvement led to favorable attitudes toward the site.

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Science.gov Websites

Search skip specific nav links Home arrow About ACHP arrow Web Site Privacy Policy ACHP Web Site Privacy be used after its purpose has been fulfilled. For questions on our Web site privacy policy, please contact the Web manager. Updated October 2, 2006 Return to Top

Satellite Contamination and Materials Outgassing Knowledgebase - An Interactive Database Reference

NASA Technical Reports Server (NTRS)

Green, D. B.; Burns, Dewitt (Technical Monitor)

2001-01-01

The goal of this program is to collect at one site much of the knowledge accumulated about the outgassing properties of aerospace materials based on ground testing, the effects of this outgassing observed on spacecraft in flight, and the broader contamination environment measured by instruments on-orbit. We believe that this Web site will help move contamination a step forward, away from anecdotal folklore toward engineering discipline. Our hope is that once operational, this site will form a nucleus for information exchange, that users will not only take information from our knowledge base, but also provide new information from ground testing and space missions, expanding and increasing the value of this site to all. We urge Government and industry users to endorse this approach that will reduce redundant testing, reduce unnecessary delays, permit uniform comparisons, and permit informed decisions.

A Two-Tiered Model for Analyzing Library Web Site Usage Statistics, Part 1: Web Server Logs.

ERIC Educational Resources Information Center

Cohen, Laura B.

2003-01-01

Proposes a two-tiered model for analyzing web site usage statistics for academic libraries: one tier for library administrators that analyzes measures indicating library use, and a second tier for web site managers that analyzes measures aiding in server maintenance and site design. Discusses the technology of web site usage statistics, and…

Analysis of governmental Web sites on food safety issues: a global perspective.

PubMed

Namkung, Young; Almanza, Barbara A

2006-10-01

Despite a growing concern over food safety issues, as well as a growing dependence on the Internet as a source of information, little research has been done to examine the presence and relevance of food safety-related information on Web sites. The study reported here conducted Web site analysis in order to examine the current operational status of governmental Web sites on food safety issues. The study also evaluated Web site usability, especially information dimensionalities such as utility, currency, and relevance of content, from the perspective of the English-speaking consumer. Results showed that out of 192 World Health Organization members, 111 countries operated governmental Web sites that provide information about food safety issues. Among 171 searchable Web sites from the 111 countries, 123 Web sites (71.9 percent) were accessible, and 81 of those 123 (65.9 percent) were available in English. The majority of Web sites offered search engine tools and related links for more information, but their availability and utility was limited. In terms of content, 69.9 percent of Web sites offered information on foodborne-disease outbreaks, compared with 31.5 percent that had travel- and health-related information.

A database for the monitoring of thermal anomalies over the Amazon forest and adjacent intertropical oceans

PubMed Central

Jiménez-Muñoz, Juan C.; Mattar, Cristian; Sobrino, José A.; Malhi, Yadvinder

2015-01-01

Advances in information technologies and accessibility to climate and satellite data in recent years have favored the development of web-based tools with user-friendly interfaces in order to facilitate the dissemination of geo/biophysical products. These products are useful for the analysis of the impact of global warming over different biomes. In particular, the study of the Amazon forest responses to drought have recently received attention by the scientific community due to the occurrence of two extreme droughts and sustained warming over the last decade. Thermal Amazoni@ is a web-based platform for the visualization and download of surface thermal anomalies products over the Amazon forest and adjacent intertropical oceans using Google Earth as a baseline graphical interface (http://ipl.uv.es/thamazon/web). This platform is currently operational at the servers of the University of Valencia (Spain), and it includes both satellite (MODIS) and climatic (ERA-Interim) datasets. Thermal Amazoni@ is composed of the viewer system and the web and ftp sites with ancillary information and access to product download. PMID:26029379

A database for the monitoring of thermal anomalies over the Amazon forest and adjacent intertropical oceans.

PubMed

Jiménez-Muñoz, Juan C; Mattar, Cristian; Sobrino, José A; Malhi, Yadvinder

2015-01-01

Advances in information technologies and accessibility to climate and satellite data in recent years have favored the development of web-based tools with user-friendly interfaces in order to facilitate the dissemination of geo/biophysical products. These products are useful for the analysis of the impact of global warming over different biomes. In particular, the study of the Amazon forest responses to drought have recently received attention by the scientific community due to the occurrence of two extreme droughts and sustained warming over the last decade. Thermal Amazoni@ is a web-based platform for the visualization and download of surface thermal anomalies products over the Amazon forest and adjacent intertropical oceans using Google Earth as a baseline graphical interface (http://ipl.uv.es/thamazon/web). This platform is currently operational at the servers of the University of Valencia (Spain), and it includes both satellite (MODIS) and climatic (ERA-Interim) datasets. Thermal Amazoni@ is composed of the viewer system and the web and ftp sites with ancillary information and access to product download.

Alaska Geochemical Database - Mineral Exploration Tool for the 21st Century - PDF of presentation

USGS Publications Warehouse

Granitto, Matthew; Schmidt, Jeanine M.; Labay, Keith A.; Shew, Nora B.; Gamble, Bruce M.

2012-01-01

The U.S. Geological Survey has created a geochemical database of geologic material samples collected in Alaska. This database is readily accessible to anyone with access to the Internet. Designed as a tool for mineral or environmental assessment, land management, or mineral exploration, the initial version of the Alaska Geochemical Database - U.S. Geological Survey Data Series 637 - contains geochemical, geologic, and geospatial data for 264,158 samples collected from 1962-2009: 108,909 rock samples; 92,701 sediment samples; 48,209 heavy-mineral-concentrate samples; 6,869 soil samples; and 7,470 mineral samples. In addition, the Alaska Geochemical Database contains mineralogic data for 18,138 nonmagnetic-fraction heavy mineral concentrates, making it the first U.S. Geological Survey database of this scope that contains both geochemical and mineralogic data. Examples from the Alaska Range will illustrate potential uses of the Alaska Geochemical Database in mineral exploration. Data from the Alaska Geochemical Database have been extensively checked for accuracy of sample media description, sample site location, and analytical method using U.S. Geological Survey sample-submittal archives and U.S. Geological Survey publications (plus field notebooks and sample site compilation base maps from the Alaska Technical Data Unit in Anchorage, Alaska). The database is also the repository for nearly all previously released U.S. Geological Survey Alaska geochemical datasets. Although the Alaska Geochemical Database is a fully relational database in Microsoft® Access 2003 and 2010 formats, these same data are also provided as a series of spreadsheet files in Microsoft® Excel 2003 and 2010 formats, and as ASCII text files. A DVD version of the Alaska Geochemical Database was released in October 2011, as U.S. Geological Survey Data Series 637, and data downloads are available at http://pubs.usgs.gov/ds/637/. Also, all Alaska Geochemical Database data have been incorporated into the interactive U.S. Geological Survey Mineral Resource Data web portal, available at http://mrdata.usgs.gov/.

REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

PubMed

Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

2011-03-01

RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/. Copyright © 2010 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Subject and authorship of records related to the Organization for Tropical Studies (OTS) in BINABITROP, a comprehensive database about Costa Rican biology.

PubMed

Monge-Nájera, Julián; Nielsen-Muñoz, Vanessa; Azofeifa-Mora, Ana Beatriz

2013-06-01

BINABITROP is a bibliographical database of more than 38000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces) and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011). Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.

WebEAV

PubMed Central

Nadkarni, Prakash M.; Brandt, Cynthia M.; Marenco, Luis

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples. PMID:10887163

Spatial Digital Database for the Geology of the San Pedro River Basin in Cochise, Gila, Graham, Pima, and Pinal Counties, Arizona

USGS Publications Warehouse

Bolm, Karen S.

2002-01-01

The map area is located in southeastern Arizona. This report describes the map units, the methods used to convert the geologic map data into a digital format, and the ArcInfo GIS file structures and relationships; and it explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. See figures 2 and 3 for page-size versions of the map compilation.

The Arctic Observing Viewer: A Web-mapping Application for U.S. Arctic Observing Activities

NASA Astrophysics Data System (ADS)

Kassin, A.; Gaylord, A. G.; Manley, W. F.; Villarreal, S.; Tweedie, C. E.; Cody, R. P.; Copenhaver, W.; Dover, M.; Score, R.; Habermann, T.

2014-12-01

Although a great deal of progress has been made with various arctic observing efforts, it can be difficult to assess such progress when so many agencies, organizations, research groups and others are making such rapid progress. To help meet the strategic needs of the U.S. SEARCH-AON program and facilitate the development of SAON and related initiatives, the Arctic Observing Viewer (AOV; http://ArcticObservingViewer.org) has been developed. This web mapping application compiles detailed information pertaining to U.S. Arctic Observing efforts. Contributing partners include the U.S. NSF, USGS, ACADIS, ADIwg, AOOS, a2dc, AON, ARMAP, BAID, IASOA, INTERACT, and others. Over 6100 sites are currently in the AOV database and the application allows users to visualize, navigate, select, advance search, draw, print, and more. AOV is founded on principles of software and data interoperability and includes an emerging "Project" metadata standard, which uses ISO 19115-1 and compatible web services. In the last year, substantial efforts have focused on maintaining and centralizing all database information. In order to keep up with emerging technologies and demand for the application, the AOV data set has been structured and centralized within a relational database; furthermore, the application front-end has been ported to HTML5. Porting the application to HTML5 will now provide access to mobile users utilizing tablets and cell phone devices. Other application enhancements include an embedded Apache Solr search platform which provides users with the capability to perform advance searches throughout the AOV dataset, and an administration web based data management system which allows the administrators to add, update, and delete data in real time. We encourage all collaborators to use AOV tools and services for their own purposes and to help us extend the impact of our efforts and ensure AOV complements other cyber-resources. Reinforcing dispersed but interoperable resources in this way will help to ensure improved capacities for conducting activities such as assessing the status of arctic observing efforts, optimizing logistic operations, and for quickly accessing external and project-focused web resources for more detailed information and data.

TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

PubMed

Sonar, Krushna; Kabra, Ritika; Singh, Shailza

2018-03-12

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms. This web resource further allows to compute a phylogenetic tree by performing multiple sequence alignment (MSA) using CLUSTALW suite embedded in it. Also, cross-linking to other databases helps in gathering more information for a certain transport protein in a single website.

ACHP | Other Historic Preservation Web Sites of Interest

Science.gov Websites

Preservation Web Sites of Interest Other Historic Preservation Web Sites of Interest National Transportation an organization's link on the ACHP's Web site does not imply endorsement of the organization or its

DaVIE: Database for the Visualization and Integration of Epigenetic data

PubMed Central

Fejes, Anthony P.; Jones, Meaghan J.; Kobor, Michael S.

2014-01-01

One of the challenges in the analysis of large data sets, particularly in a population-based setting, is the ability to perform comparisons across projects. This has to be done in such a way that the integrity of each individual project is maintained, while ensuring that the data are comparable across projects. These issues are beginning to be observed in human DNA methylation studies, as the Illumina 450k platform and next generation sequencing-based assays grow in popularity and decrease in price. This increase in productivity is enabling new insights into epigenetics, but also requires the development of pipelines and software capable of handling the large volumes of data. The specific problems inherent in creating a platform for the storage, comparison, integration, and visualization of DNA methylation data include data storage, algorithm efficiency and ability to interpret the results to derive biological meaning from them. Databases provide a ready-made solution to these issues, but as yet no tools exist that that leverage these advantages while providing an intuitive user interface for interpreting results in a genomic context. We have addressed this void by integrating a database to store DNA methylation data with a web interface to query and visualize the database and a set of libraries for more complex analysis. The resulting platform is called DaVIE: Database for the Visualization and Integration of Epigenetics data. DaVIE can use data culled from a variety of sources, and the web interface includes the ability to group samples by sub-type, compare multiple projects and visualize genomic features in relation to sites of interest. We have used DaVIE to identify patterns of DNA methylation in specific projects and across different projects, identify outlier samples, and cross-check differentially methylated CpG sites identified in specific projects across large numbers of samples. A demonstration server has been setup using GEO data at http://echelon.cmmt.ubc.ca/dbaccess/, with login “guest” and password “guest.” Groups may download and install their own version of the server following the instructions on the project's wiki. PMID:25278960

Using Web Database Tools To Facilitate the Construction of Knowledge in Online Courses.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of database tools that dynamically generate World Wide Web materials and focuses on the use of these tools to support research activities, as well as teaching and learning. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and e-commerce have…

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

PubMed

Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

2008-02-01

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

Metadata tables to enable dynamic data modeling and web interface design: the SEER example.

PubMed

Weiner, Mark; Sherr, Micah; Cohen, Abigail

2002-04-01

A wealth of information addressing health status, outcomes and resource utilization is compiled and made available by various government agencies. While exploration of the data is possible using existing tools, in general, would-be users of the resources must acquire CD-ROMs or download data from the web, and upload the data into their own database. Where web interfaces exist, they are highly structured, limiting the kinds of queries that can be executed. This work develops a web-based database interface engine whose content and structure is generated through interaction with a metadata table. The result is a dynamically generated web interface that can easily accommodate changes in the underlying data model by altering the metadata table, rather than requiring changes to the interface code. This paper discusses the background and implementation of the metadata table and web-based front end and provides examples of its use with the NCI's Surveillance, Epidemiology and End-Results (SEER) database.

Evaluating Domestic and International Web-Site Strategies.

ERIC Educational Resources Information Center

Simeon, Roblyn

1999-01-01

Presents the AIPD (attracting, informing, positioning, and delivering) approach to the evaluation of commercial Web sites that assess the strategic potential of Web sites, provides a framework for the development of competitive sites, and compares Web site strategies within and across national boundaries. Compares Internet strategies of Japanese…

CUNY+ Web: Usability Study of the Web-Based GUI Version of the Bibliographic Database of the City University of New York (CUNY).

ERIC Educational Resources Information Center

Oulanov, Alexei; Pajarillo, Edmund J. Y.

2002-01-01

Describes the usability evaluation of the CUNY (City University of New York) information system in Web and Graphical User Interface (GUI) versions. Compares results to an earlier usability study of the basic information database available on CUNY's wide-area network and describes the applicability of the previous usability instrument to this…

The integrated web service and genome database for agricultural plants with biotechnology information.

PubMed

Kim, Changkug; Park, Dongsuk; Seol, Youngjoo; Hahn, Jangho

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage.

77 FR 74266 - Review of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-13

... of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site AGENCY... review is now available on the FHWA Web site, http://www.fhwa.dot.gov/map21 , and FTA Web site, http://www.fta.dot.gov/map21 . DATES: These reports were posted on the Web site on December 7, 2012...

10 CFR 905.23 - What are the opportunities for using the Freedom of Information Act to request plan and report data?

Code of Federal Regulations, 2010 CFR

2010-01-01

...'s publicly available Web site or on Western's Web site. Customers posting their IRPs on their own Web site must notify Western of this decision when they submit their IRP. A hotlink on Western's Web site to IRPs posted on customer Web sites gives interested parties ready access to those IRPs. Western...

10 CFR 905.23 - What are the opportunities for using the Freedom of Information Act to request plan and report data?

Code of Federal Regulations, 2014 CFR

2014-01-01

...'s publicly available Web site or on Western's Web site. Customers posting their IRPs on their own Web site must notify Western of this decision when they submit their IRP. A hotlink on Western's Web site to IRPs posted on customer Web sites gives interested parties ready access to those IRPs. Western...

10 CFR 905.23 - What are the opportunities for using the Freedom of Information Act to request plan and report data?

Code of Federal Regulations, 2011 CFR

2011-01-01

...'s publicly available Web site or on Western's Web site. Customers posting their IRPs on their own Web site must notify Western of this decision when they submit their IRP. A hotlink on Western's Web site to IRPs posted on customer Web sites gives interested parties ready access to those IRPs. Western...

10 CFR 905.23 - What are the opportunities for using the Freedom of Information Act to request plan and report data?

Code of Federal Regulations, 2012 CFR

2012-01-01

...'s publicly available Web site or on Western's Web site. Customers posting their IRPs on their own Web site must notify Western of this decision when they submit their IRP. A hotlink on Western's Web site to IRPs posted on customer Web sites gives interested parties ready access to those IRPs. Western...

10 CFR 905.23 - What are the opportunities for using the Freedom of Information Act to request plan and report data?

Code of Federal Regulations, 2013 CFR

2013-01-01

...'s publicly available Web site or on Western's Web site. Customers posting their IRPs on their own Web site must notify Western of this decision when they submit their IRP. A hotlink on Western's Web site to IRPs posted on customer Web sites gives interested parties ready access to those IRPs. Western...

Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD): Data and Tools for Dynamic Management and Decision Support

NASA Technical Reports Server (NTRS)

Humphries, G. R. W.; Naveen, R.; Schwaller, M.; Che-Castaldo, C.; McDowall, P.; Schrimpf, M.; Schrimpf, Michael; Lynch, H. J.

2017-01-01

The Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) is a web-based, open access, decision-support tool designed to assist scientists, non-governmental organizations and policy-makers working to meet the management objectives as set forth by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) and other components of the Antarctic Treaty System (ATS) (that is, Consultative Meetings and the ATS Committee on Environmental Protection). MAPPPD was designed specifically to complement existing efforts such as the CCAMLR Ecosystem Monitoring Program (CEMP) and the ATS site guidelines for visitors. The database underlying MAPPPD includes all publicly available (published and unpublished) count data on emperor, gentoo, Adelie) and chinstrap penguins in Antarctica. Penguin population models are used to assimilate available data into estimates of abundance for each site and year.Results are easily aggregated across multiple sites to obtain abundance estimates over any user-defined area of interest. A front end web interface located at www.penguinmap.com provides free and ready access to the most recent count and modelled data, and can act as a facilitator for data transfer between scientists and Antarctic stakeholders to help inform management decisions for the continent.