Mercury Toolset for Spatiotemporal Metadata

NASA Technical Reports Server (NTRS)

Wilson, Bruce E.; Palanisamy, Giri; Devarakonda, Ranjeet; Rhyne, B. Timothy; Lindsley, Chris; Green, James

2010-01-01

Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily) harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

Mercury Toolset for Spatiotemporal Metadata

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce; Rhyne, B. Timothy; Lindsley, Chris

2010-06-01

Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily)harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

Mercury: Reusable software application for Metadata Management, Data Discovery and Access

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce E.

2009-12-01

Mercury is a federated metadata harvesting, data discovery and access tool based on both open source packages and custom developed software. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury is itself a reusable toolset for metadata, with current use in 12 different projects. Mercury also supports the reuse of metadata by enabling searching across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. Mercury provides a single portal to information contained in distributed data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. One of the major goals of the recent redesign of Mercury was to improve the software reusability across the projects which currently fund the continuing development of Mercury. These projects span a range of land, atmosphere, and ocean ecological communities and have a number of common needs for metadata searches, but they also have a number of needs specific to one or a few projects To balance these common and project-specific needs, Mercury’s architecture includes three major reusable components; a harvester engine, an indexing system and a user interface component. The harvester engine is responsible for harvesting metadata records from various distributed servers around the USA and around the world. The harvester software was packaged in such a way that all the Mercury projects will use the same harvester scripts but each project will be driven by a set of configuration files. The harvested files are then passed to the Indexing system, where each of the fields in these structured metadata records are indexed properly, so that the query engine can perform simple, keyword, spatial and temporal searches across these metadata sources. The search user interface software has two API categories; a common core API which is used by all the Mercury user interfaces for querying the index and a customized API for project specific user interfaces. For our work in producing a reusable, portable, robust, feature-rich application, Mercury received a 2008 NASA Earth Science Data Systems Software Reuse Working Group Peer-Recognition Software Reuse Award. The new Mercury system is based on a Service Oriented Architecture and effectively reuses components for various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. The software also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets, integrated shopping cart to order datasets from various data centers (ORNL DAAC, NSIDC) and integrated visualization tools. Other features include: Filtering and dynamic sorting of search results, book-markable search results, save, retrieve, and modify search criteria.

Internet Medline providers.

PubMed

Vine, D L; Coady, T R

1998-01-01

Each database in this review has features that will appeal to some users. Each provides a credible interface to information available within the Medline database. The major differences are pricing and interface design. In this context, features that cost more and might seem trivial to the occasional searcher may actually save time and money when used by the professional. Internet Grateful Med is free, but Ms. Coady and I agree the availability of only three ANDable search fields is a major functional limitation. PubMed is also free but much more powerful. The command line interface that permits very sophisticated searches requires a commitment that casual users will find intimidating. Ms. Coady did not believe the feedback currently provided during a search was sufficient for sustained professional use. Paper Chase and Knowledge Finder are mature, modestly priced Medline search services. Paper Chase provides a menu-driven interface that is very easy to use, yet permits the user to search virtually all of Medline's data fields. Knowledge Finder emphasizes the use of natural language queries but fully supports more traditional search strategies. The impact of the tradeoff between fuzzy and Boolean strategies offered by Knowledge Finder is unclear and beyond the scope of this review. Additional software must be downloaded to use all of Knowledge Finders' features. Other providers required no software beyond the basic Internet browser, and this requirement prevented Ms. Coady from evaluating Knowledge Finder. Ovid and Silver Platter offer well-designed interfaces that simplify the construction of complex queries. These are clearly services designed for professional users. While pricing eliminates these for casual use, it should be emphasized that Medline citation access is only a portion of the service provided by these high-end vendors. Finally, we should comment that each of the vendors and government-sponsored services provided prompt and useful feedback to e-mail questions about usage. In conclusion, we would suggest you try the various services, determine which interface suits your style and budget, then perform simple searches until you learn the strengths and weaknesses of the service you select.

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.

PubMed

Sandhu, Maninder; Sureshkumar, V; Prakash, Chandra; Dixit, Rekha; Solanke, Amolkumar U; Sharma, Tilak Raj; Mohapatra, Trilochan; S V, Amitha Mithra

2017-09-30

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. 'Physical position search' is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the 'common genes across varieties' search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201.

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.

WCSTools 3.0: More Tools for Image Astrometry and Catalog Searching

NASA Astrophysics Data System (ADS)

Mink, Douglas J.

For five years, WCSTools has provided image astrometry for astronomers who need accurate positions for objects they wish to observe. Other functions have been added and improved since the package was first released. Support has been added for new catalogs, such as the GSC-ACT, 2MASS Point Source Catalog, and GSC II, as they have been published. A simple command line interface can search any supported catalog, returning information in several standard formats, whether the catalog is on a local disk or searchable over the World Wide Web. The catalog searching routine can be located on either end (or both ends!) of such a web connection, and the output from one catalog search can be used as the input to another search.

A Simple and Customizable Web Interface to the Virtual Solar Observatory

NASA Astrophysics Data System (ADS)

Hughitt, V. Keith; Hourcle, J.; Suarez-Sola, I.; Davey, A.

2010-05-01

As the variety and number of solar data sources continue to increase at a rapid rate, the importance of providing methods to search through these sources becomes increasingly important. By taking advantage of the power of modern JavaScript libraries, a new version of the Virtual Solar Observatory's web interface aims to provide a significantly faster and simpler way to explore the multitude of data repositories available. Querying asynchroniously serves not only to eliminates bottlenecks resulting from slow or unresponsive data providers, but also allows for displaying of results as soon as they are returned. Implicit pagination and post-query filtering enables users to work with large result-sets, while a more modular and customizable UI provides a mechanism for customizing both the look-and-feel and behavior of the VSO web interface. Finally, the new web interface features a custom widget system capable of displaying additional tools and information along-side of the standard VSO search form. Interested users can also write their own widgets and submit them for future incorporation into VSO.

Mercury: An Example of Effective Software Reuse for Metadata Management, Data Discovery and Access

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce E.

2008-12-01

Mercury is a federated metadata harvesting, data discovery and access tool based on both open source packages and custom developed software. Though originally developed for NASA, the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports the reuse of metadata by enabling searching across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. Mercury provides a single portal to information contained in distributed data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. One of the major goals of the recent redesign of Mercury was to improve the software reusability across the 12 projects which currently fund the continuing development of Mercury. These projects span a range of land, atmosphere, and ocean ecological communities and have a number of common needs for metadata searches, but they also have a number of needs specific to one or a few projects. To balance these common and project-specific needs, Mercury's architecture has three major reusable components; a harvester engine, an indexing system and a user interface component. The harvester engine is responsible for harvesting metadata records from various distributed servers around the USA and around the world. The harvester software was packaged in such a way that all the Mercury projects will use the same harvester scripts but each project will be driven by a set of project specific configuration files. The harvested files are structured metadata records that are indexed against the search library API consistently, so that it can render various search capabilities such as simple, fielded, spatial and temporal. This backend component is supported by a very flexible, easy to use Graphical User Interface which is driven by cascading style sheets, which make it even simpler for reusable design implementation. The new Mercury system is based on a Service Oriented Architecture and effectively reuses components for various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. The software also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets, integrated shopping cart to order datasets from various data centers (ORNL DAAC, NSIDC) and integrated visualization tools. Other features include: Filtering and dynamic sorting of search results, book- markable search results, save, retrieve, and modify search criteria.

Using a Simple Knowledge Organization System to facilitate Catalogue and Search for the ESA CCI Open Data Portal

NASA Astrophysics Data System (ADS)

Wilson, Antony; Bennett, Victoria; Donegan, Steve; Juckes, Martin; Kershaw, Philip; Petrie, Ruth; Stephens, Ag; Waterfall, Alison

2016-04-01

The ESA Climate Change Initiative (CCI) is a €75m programme that runs from 2009-2016, with a goal to provide stable, long-term, satellite-based essential climate variable (ECV) data products for climate modellers and researchers. As part of the CCI, ESA have funded the Open Data Portal project to establish a central repository to bring together the data from these multiple sources and make it available in a consistent way, in order to maximise its dissemination amongst the international user community. Search capabilities are a critical component to attaining this goal. To this end, the project is providing dataset-level metadata in the form of ISO 19115 records served via a standard OGC CSW interface. In addition, the Open Data Portal is re-using the search system from the Earth System Grid Federation (ESGF), successfully applied to support CMIP5 (5th Coupled Model Intercomparison Project) and obs4MIPs. This uses a tightly defined controlled vocabulary of metadata terms, the DRS (The Data Reference Syntax) which encompass different aspects of the data. This system hs facilitated the construction of a powerful faceted search interface to enable users to discover data at the individual file level of granularity through ESGF's web portal frontend. The use of a consistent set of model experiments for CMIP5 allowed the definition of a uniform DRS for all model data served from ESGF. For CCI however, there are thirteen ECVs, each of which is derived from multiple sources and different science communities resulting in highly heterogeneous metadata. An analysis has been undertaken of the concepts in use, with the aim to produce a CCI DRS which could be provide a single authoritative source for cataloguing and searching the CCI data for the Open Data Portal. The use of SKOS (Simple Knowledge Organization System) and OWL (Web Ontology Language) to represent the DRS are a natural fit and provide controlled vocabularies as well as a way to represent relationships between similar terms used in different ECVs. An iterative approach has been adopted for the model development working closely with domain experts and drawing on practical experience working with content in the input datasets. Tooling has been developed to enable the definition of vocabulary terms via a simple spreadsheet format which can then be automatically converted into Turtle notation and uploaded to the CCI DRS vocabulary service. With a baseline model established, work is underway to develop an ingestion pipeline to import validated search metadata into the ESGF and OGC CSW search services. In addition to the search terms indexed into the ESGF search system, ISO 19115 records will also be similarly tagged during this process with search terms from the data model. In this way it will be possible to construct a faceted search user interface for the Portal which can yield linked search results for data both at the file and dataset level granularity. It is hoped that this will also provide a rich range of content for third-party organisations wishing to incorporate access to CCI data in their own applications and services.

HOWDY: an integrated database system for human genome research

PubMed Central

Hirakawa, Mika

2002-01-01

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search. PMID:11752279

Chandra Source Catalog: User Interfaces

NASA Astrophysics Data System (ADS)

Bonaventura, Nina; Evans, I. N.; Harbo, P. N.; Rots, A. H.; Tibbetts, M. S.; Van Stone, D. W.; Zografou, P.; Anderson, C. S.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Evans, J. D.; Fabbiano, G.; Galle, E.; Gibbs, D. G.; Glotfelty, K. J.; Grier, J. D.; Hain, R.; Hall, D. M.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McCollough, M. L.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Nowak, M. A.; Plummer, D. A.; Primini, F. A.; Refsdal, B. L.; Siemiginowska, A. L.; Sundheim, B. A.; Winkelman, S. L.

2010-03-01

The CSCview data mining interface is available for browsing the Chandra Source Catalog (CSC) and downloading tables of quality-assured source properties and data products. Once the desired source properties and search criteria are entered into the CSCview query form, the resulting source matches are returned in a table along with the values of the requested source properties for each source. (The catalog can be searched on any source property, not just position.) At this point, the table of search results may be saved to a text file, and the available data products for each source may be downloaded. CSCview save files are output in RDB-like and VOTable format. The available CSC data products include event files, spectra, lightcurves, and images, all of which are processed with the CIAO software. CSC data may also be accessed non-interactively with Unix command-line tools such as cURL and Wget, using ADQL 2.0 query syntax. In fact, CSCview features a separate ADQL query form for those who wish to specify this type of query within the GUI. Several interfaces are available for learning if a source is included in the catalog (in addition to CSCview): 1) the CSC interface to Sky in Google Earth shows the footprint of each Chandra observation on the sky, along with the CSC footprint for comparison (CSC source properties are also accessible when a source within a Chandra field-of-view is clicked); 2) the CSC Limiting Sensitivity online tool indicates if a source at an input celestial location was too faint for detection; 3) an IVOA Simple Cone Search interface locates all CSC sources within a specified radius of an R.A. and Dec.; and 4) the CSC-SDSS cross-match service returns the list of sources common to the CSC and SDSS, either all such sources or a subset based on search criteria.

Migration to Earth Observation Satellite Product Dissemination System at JAXA

NASA Astrophysics Data System (ADS)

Ikehata, Y.; Matsunaga, M.

2017-12-01

JAXA released "G-Portal" as a portal web site for search and deliver data of Earth observation satellites in February 2013. G-Portal handles ten satellites data; GPM, TRMM, Aqua, ADEOS-II, ALOS (search only), ALOS-2 (search only), MOS-1, MOS-1b, ERS-1 and JERS-1 and archives 5.17 million products and 14 million catalogues in total. Users can search those products/catalogues in GUI web search and catalogue interface(CSW/Opensearch). In this fiscal year, we will replace this to "Next G-Portal" and has been doing integration, test and migrations. New G-Portal will treat data of satellites planned to be launched in the future in addition to those handled by G - Portal. At system architecture perspective, G-Portal adopted "cluster system" for its redundancy, so we must replace the servers into those with higher specifications when we improve its performance ("scale up approach"). This requests a lot of cost in every improvement. To avoid this, Next G-Portal adopts "scale out" system: load balancing interfaces, distributed file system, distributed data bases. (We reported in AGU fall meeting 2015(IN23D-1748).) At customer usability perspective, G-Portal provides complicated interface: "step by step" web design, randomly generated URLs, sftp (needs anomaly tcp port). Customers complained about the interfaces and the support team had been tired from answering them. To solve this problem, Next G-Portal adopts simple interfaces: "1 page" web design, RESTful URL, and Normal FTP. (We reported in AGU fall meeting 2016(IN23B-1778).) Furthermore, Next G-Portal must merge GCOM-W data dissemination system to be terminated in the next March as well as the current G-Portal. This might arrise some difficulties, since the current G-Portal and GCOM-W data dissemination systems are quite different from Next G-Portal. The presentation reports the knowledge obtained from the process of merging those systems.

Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

ERIC Educational Resources Information Center

Fitzgibbons, Megan; Meert, Deborah

2010-01-01

The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

Evidence-based Medicine Search: a customizable federated search engine.

PubMed

Bracke, Paul J; Howse, David K; Keim, Samuel M

2008-04-01

This paper reports on the development of a tool by the Arizona Health Sciences Library (AHSL) for searching clinical evidence that can be customized for different user groups. The AHSL provides services to the University of Arizona's (UA's) health sciences programs and to the University Medical Center. Librarians at AHSL collaborated with UA College of Medicine faculty to create an innovative search engine, Evidence-based Medicine (EBM) Search, that provides users with a simple search interface to EBM resources and presents results organized according to an evidence pyramid. EBM Search was developed with a web-based configuration component that allows the tool to be customized for different specialties. Informal and anecdotal feedback from physicians indicates that EBM Search is a useful tool with potential in teaching evidence-based decision making. While formal evaluation is still being planned, a tool such as EBM Search, which can be configured for specific user populations, may help lower barriers to information resources in an academic health sciences center.

Evidence-based Medicine Search: a customizable federated search engine

PubMed Central

Bracke, Paul J.; Howse, David K.; Keim, Samuel M.

2008-01-01

Purpose: This paper reports on the development of a tool by the Arizona Health Sciences Library (AHSL) for searching clinical evidence that can be customized for different user groups. Brief Description: The AHSL provides services to the University of Arizona's (UA's) health sciences programs and to the University Medical Center. Librarians at AHSL collaborated with UA College of Medicine faculty to create an innovative search engine, Evidence-based Medicine (EBM) Search, that provides users with a simple search interface to EBM resources and presents results organized according to an evidence pyramid. EBM Search was developed with a web-based configuration component that allows the tool to be customized for different specialties. Outcomes/Conclusion: Informal and anecdotal feedback from physicians indicates that EBM Search is a useful tool with potential in teaching evidence-based decision making. While formal evaluation is still being planned, a tool such as EBM Search, which can be configured for specific user populations, may help lower barriers to information resources in an academic health sciences center. PMID:18379665

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

PubMed Central

Kinjo, Akira R.; Yamashita, Reiko; Nakamura, Haruki

2010-01-01

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/ PMID:20798081

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

PubMed

Kinjo, Akira R; Yamashita, Reiko; Nakamura, Haruki

2010-08-25

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/

OpenSearch (ECHO-ESIP) & REST API for Earth Science Data Access

NASA Astrophysics Data System (ADS)

Mitchell, A.; Cechini, M.; Pilone, D.

2010-12-01

This presentation will provide a brief technical overview of OpenSearch, the Earth Science Information Partners (ESIP) Federated Search framework, and the REST architecture; discuss NASA’s Earth Observing System (EOS) ClearingHOuse’s (ECHO) implementation lessons learned; and demonstrate the simplified usage of these technologies. SOAP, as a framework for web service communication has numerous advantages for Enterprise applications and Java/C# type programming languages. As a technical solution, SOAP has been a reliable framework on top of which many applications have been successfully developed and deployed. However, as interest grows for quick development cycles and more intriguing “mashups,” the SOAP API loses its appeal. Lightweight and simple are the vogue characteristics that are sought after. Enter the REST API architecture and OpenSearch format. Both of these items provide a new path for application development addressing some of the issues unresolved by SOAP. ECHO has made available all of its discovery, order submission, and data management services through a publicly accessible SOAP API. This interface is utilized by a variety of ECHO client and data partners to provide valuable capabilities to end users. As ECHO interacted with current and potential partners looking to develop Earth Science tools utilizing ECHO, it became apparent that the development overhead required to interact with the SOAP API was a growing barrier to entry. ECHO acknowledged the technical issues that were being uncovered by its partner community and chose to provide two new interfaces for interacting with the ECHO metadata catalog. The first interface is built upon the OpenSearch format and ESIP Federated Search framework. Leveraging these two items, a client (ECHO-ESIP) was developed with a focus on simplified searching and results presentation. The second interface is built upon the Representational State Transfer (REST) architecture. Leveraging the REST architecture, a new API has been made available that will provide access to the entire SOAP API suite of services. The results of these development activities has not only positioned to engage in the thriving world of mashup applications, but also provided an excellent real-world case study of how to successfully leverage these emerging technologies.

Building a better search engine for earth science data

NASA Astrophysics Data System (ADS)

Armstrong, E. M.; Yang, C. P.; Moroni, D. F.; McGibbney, L. J.; Jiang, Y.; Huang, T.; Greguska, F. R., III; Li, Y.; Finch, C. J.

2017-12-01

Free text data searching of earth science datasets has been implemented with varying degrees of success and completeness across the spectrum of the 12 NASA earth sciences data centers. At the JPL Physical Oceanography Distributed Active Archive Center (PO.DAAC) the search engine has been developed around the Solr/Lucene platform. Others have chosen other popular enterprise search platforms like Elasticsearch. Regardless, the default implementations of these search engines leveraging factors such as dataset popularity, term frequency and inverse document term frequency do not fully meet the needs of precise relevancy and ranking of earth science search results. For the PO.DAAC, this shortcoming has been identified for several years by its external User Working Group that has assigned several recommendations to improve the relevancy and discoverability of datasets related to remotely sensed sea surface temperature, ocean wind, waves, salinity, height and gravity that comprise a total count of over 500 public availability datasets. Recently, the PO.DAAC has teamed with an effort led by George Mason University to improve the improve the search and relevancy ranking of oceanographic data via a simple search interface and powerful backend services called MUDROD (Mining and Utilizing Dataset Relevancy from Oceanographic Datasets to Improve Data Discovery) funded by the NASA AIST program. MUDROD has mined and utilized the combination of PO.DAAC earth science dataset metadata, usage metrics, and user feedback and search history to objectively extract relevance for improved data discovery and access. In addition to improved dataset relevance and ranking, the MUDROD search engine also returns recommendations to related datasets and related user queries. This presentation will report on use cases that drove the architecture and development, and the success metrics and improvements on search precision and recall that MUDROD has demonstrated over the existing PO.DAAC search interfaces.

Thesaurus-Enhanced Search Interfaces.

ERIC Educational Resources Information Center

Shiri, Ali Asghar; Revie, Crawford; Chowdhury, Gobinda

2002-01-01

Discussion of user interfaces to information retrieval systems focuses on interfaces that incorporate thesauri as part of their searching and browsing facilities. Discusses research literature related to information searching behavior, information retrieval interface evaluation, search term selection, and query expansion; and compares thesaurus…

Search of the Deep and Dark Web via DARPA Memex

NASA Astrophysics Data System (ADS)

Mattmann, C. A.

2015-12-01

Search has progressed through several stages due to the increasing size of the Web. Search engines first focused on text and its rate of occurrence; then focused on the notion of link analysis and citation then on interactivity and guided search; and now on the use of social media - who we interact with, what we comment on, and who we follow (and who follows us). The next stage, referred to as "deep search," requires solutions that can bring together text, images, video, importance, interactivity, and social media to solve this challenging problem. The Apache Nutch project provides an open framework for large-scale, targeted, vertical search with capabilities to support all past and potential future search engine foci. Nutch is a flexible infrastructure allowing open access to ranking; URL selection and filtering approaches, to the link graph generated from search, and Nutch has spawned entire sub communities including Apache Hadoop and Apache Tika. It addresses many current needs with the capability to support new technologies such as image and video. On the DARPA Memex project, we are creating create specific extensions to Nutch that will directly improve its overall technological superiority for search and that will directly allow us to address complex search problems including human trafficking. We are integrating state-of-the-art algorithms developed by Kitware for IARPA Aladdin combined with work by Harvard to provide image and video understanding support allowing automatic detection of people and things and massive deployment via Nutch. We are expanding Apache Tika for scene understanding, object/person detection and classification in images/video. We are delivering an interactive and visual interface for initiating Nutch crawls. The interface uses Python technologies to expose Nutch data and to provide a domain specific language for crawls. With the Bokeh visualization library the interface we are delivering simple interactive crawl visualization and plotting techniques for exploring crawled information. The platform classifies, identify, and thwart predators, help to find victims and to identify buyers in human trafficking and will deliver technological superiority in search engines for DARPA. We are already transitioning the technologies into Geo and Planetary Science, and Bioinformatics.

OpenSearch technology for geospatial resources discovery

NASA Astrophysics Data System (ADS)

Papeschi, Fabrizio; Enrico, Boldrini; Mazzetti, Paolo

2010-05-01

In 2005, the term Web 2.0 has been coined by Tim O'Reilly to describe a quickly growing set of Web-based applications that share a common philosophy of "mutually maximizing collective intelligence and added value for each participant by formalized and dynamic information sharing". Around this same period, OpenSearch a new Web 2.0 technology, was developed. More properly, OpenSearch is a collection of technologies that allow publishing of search results in a format suitable for syndication and aggregation. It is a way for websites and search engines to publish search results in a standard and accessible format. Due to its strong impact on the way the Web is perceived by users and also due its relevance for businesses, Web 2.0 has attracted the attention of both mass media and the scientific community. This explosive growth in popularity of Web 2.0 technologies like OpenSearch, and practical applications of Service Oriented Architecture (SOA) resulted in an increased interest in similarities, convergence, and a potential synergy of these two concepts. SOA is considered as the philosophy of encapsulating application logic in services with a uniformly defined interface and making these publicly available via discovery mechanisms. Service consumers may then retrieve these services, compose and use them according to their current needs. A great degree of similarity between SOA and Web 2.0 may be leading to a convergence between the two paradigms. They also expose divergent elements, such as the Web 2.0 support to the human interaction in opposition to the typical SOA machine-to-machine interaction. According to these considerations, the Geospatial Information (GI) domain, is also moving first steps towards a new approach of data publishing and discovering, in particular taking advantage of the OpenSearch technology. A specific GI niche is represented by the OGC Catalog Service for Web (CSW) that is part of the OGC Web Services (OWS) specifications suite, which provides a set of services for discovery, access, and processing of geospatial resources in a SOA framework. GI-cat is a distributed CSW framework implementation developed by the ESSI Lab of the Italian National Research Council (CNR-IMAA) and the University of Florence. It provides brokering and mediation functionalities towards heterogeneous resources and inventories, exposing several standard interfaces for query distribution. This work focuses on a new GI-cat interface which allows the catalog to be queried according to the OpenSearch syntax specification, thus filling the gap between the SOA architectural design of the CSW and the Web 2.0. At the moment, there is no OGC standard specification about this topic, but an official change request has been proposed in order to enable the OGC catalogues to support OpenSearch queries. In this change request, an OpenSearch extension is proposed providing a standard mechanism to query a resource based on temporal and geographic extents. Two new catalog operations are also proposed, in order to publish a suitable OpenSearch interface. This extended interface is implemented by the modular GI-cat architecture adding a new profiling module called "OpenSearch profiler". Since GI-cat also acts as a clearinghouse catalog, another component called "OpenSearch accessor" is added in order to access OpenSearch compliant services. An important role in the GI-cat extension, is played by the adopted mapping strategy. Two different kind of mappings are required: query, and response elements mapping. Query mapping is provided in order to fit the simple OpenSearch query syntax to the complex CSW query expressed by the OGC Filter syntax. GI-cat internal data model is based on the ISO-19115 profile, that is more complex than the simple XML syndication formats, such as RSS 2.0 and Atom 1.0, suggested by OpenSearch. Once response elements are available, in order to be presented, they need to be translated from the GI-cat internal data model, to the above mentioned syndication formats; the mapping processing, is bidirectional. When GI-cat is used to access OpenSearch compliant services, the CSW query must be mapped to the OpenSearch query, and the response elements, must be translated according to the GI-cat internal data model. As results of such extensions, GI-cat provides a user friendly facade to the complex CSW interface, thus enabling it to be queried, for example, using a browser toolbar.

Central Visual Prosthesis With Interface at the Lateral Geniculate Nucleus

DTIC Science & Technology

2017-07-01

burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching...currently used in the field to implant Deep Brain Stimulation electrodes. Page 4 We thus limited ourselves to using a ‘4 French’ size split sheath...this program. At this time , several approaches for realizing the complete system have been evaluated. Initially, a very simple mechanical mockup

Distributed Computerized Catalog System

NASA Technical Reports Server (NTRS)

Borgen, Richard L.; Wagner, David A.

1995-01-01

DarkStar Distributed Catalog System describes arbitrary data objects in unified manner, providing end users with versatile, yet simple search mechanism for locating and identifying objects. Provides built-in generic and dynamic graphical user interfaces. Design of system avoids some of problems of standard DBMS, and system provides more flexibility than do conventional relational data bases, or object-oriented data bases. Data-collection lattice partly hierarchical representation of relationships among collections, subcollections, and data objects.

Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts.

PubMed

Lancaster, Owen; Beck, Tim; Atlan, David; Swertz, Morris; Thangavelu, Dhiwagaran; Veal, Colin; Dalgleish, Raymond; Brookes, Anthony J

2015-10-01

Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service. © 2015 WILEY PERIODICALS, INC.

The National Solar Observatory Digital Library - a resource for space weather studies

NASA Astrophysics Data System (ADS)

Hill, F.; Erdwurm, W.; Branston, D.; McGraw, R.

2000-09-01

We describe the National Solar Observatory Digital Library (NSODL), consisting of 200GB of on-line archived solar data, a RDBMS search engine, and an Internet HTML-form user interface. The NSODL is open to all users and provides simple access to solar physics data of basic importance for space weather research and forecasting, heliospheric research, and education. The NSODL can be accessed at the URL www.nso.noao.edu/diglib.

Designing a Visual Interface for Online Searching.

ERIC Educational Resources Information Center

Lin, Xia

1999-01-01

"MedLine Search Assistant" is a new interface for MEDLINE searching that improves both search precision and recall by helping the user convert a free text search to a controlled vocabulary-based search in a visual environment. Features of the interface are described, followed by details of the conceptual design and the physical design of…

Natural Language Search Interfaces: Health Data Needs Single-Field Variable Search.

PubMed

Jay, Caroline; Harper, Simon; Dunlop, Ian; Smith, Sam; Sufi, Shoaib; Goble, Carole; Buchan, Iain

2016-01-14

Data discovery, particularly the discovery of key variables and their inter-relationships, is key to secondary data analysis, and in-turn, the evolving field of data science. Interface designers have presumed that their users are domain experts, and so they have provided complex interfaces to support these "experts." Such interfaces hark back to a time when searches needed to be accurate first time as there was a high computational cost associated with each search. Our work is part of a governmental research initiative between the medical and social research funding bodies to improve the use of social data in medical research. The cross-disciplinary nature of data science can make no assumptions regarding the domain expertise of a particular scientist, whose interests may intersect multiple domains. Here we consider the common requirement for scientists to seek archived data for secondary analysis. This has more in common with search needs of the "Google generation" than with their single-domain, single-tool forebears. Our study compares a Google-like interface with traditional ways of searching for noncomplex health data in a data archive. Two user interfaces are evaluated for the same set of tasks in extracting data from surveys stored in the UK Data Archive (UKDA). One interface, Web search, is "Google-like," enabling users to browse, search for, and view metadata about study variables, whereas the other, traditional search, has standard multioption user interface. Using a comprehensive set of tasks with 20 volunteers, we found that the Web search interface met data discovery needs and expectations better than the traditional search. A task × interface repeated measures analysis showed a main effect indicating that answers found through the Web search interface were more likely to be correct (F1,19=37.3, P<.001), with a main effect of task (F3,57=6.3, P<.001). Further, participants completed the task significantly faster using the Web search interface (F1,19=18.0, P<.001). There was also a main effect of task (F2,38=4.1, P=.025, Greenhouse-Geisser correction applied). Overall, participants were asked to rate learnability, ease of use, and satisfaction. Paired mean comparisons showed that the Web search interface received significantly higher ratings than the traditional search interface for learnability (P=.002, 95% CI [0.6-2.4]), ease of use (P<.001, 95% CI [1.2-3.2]), and satisfaction (P<.001, 95% CI [1.8-3.5]). The results show superior cross-domain usability of Web search, which is consistent with its general familiarity and with enabling queries to be refined as the search proceeds, which treats serendipity as part of the refinement. The results provide clear evidence that data science should adopt single-field natural language search interfaces for variable search supporting in particular: query reformulation; data browsing; faceted search; surrogates; relevance feedback; summarization, analytics, and visual presentation.

Natural Language Search Interfaces: Health Data Needs Single-Field Variable Search

PubMed Central

Smith, Sam; Sufi, Shoaib; Goble, Carole; Buchan, Iain

2016-01-01

Background Data discovery, particularly the discovery of key variables and their inter-relationships, is key to secondary data analysis, and in-turn, the evolving field of data science. Interface designers have presumed that their users are domain experts, and so they have provided complex interfaces to support these “experts.” Such interfaces hark back to a time when searches needed to be accurate first time as there was a high computational cost associated with each search. Our work is part of a governmental research initiative between the medical and social research funding bodies to improve the use of social data in medical research. Objective The cross-disciplinary nature of data science can make no assumptions regarding the domain expertise of a particular scientist, whose interests may intersect multiple domains. Here we consider the common requirement for scientists to seek archived data for secondary analysis. This has more in common with search needs of the “Google generation” than with their single-domain, single-tool forebears. Our study compares a Google-like interface with traditional ways of searching for noncomplex health data in a data archive. Methods Two user interfaces are evaluated for the same set of tasks in extracting data from surveys stored in the UK Data Archive (UKDA). One interface, Web search, is “Google-like,” enabling users to browse, search for, and view metadata about study variables, whereas the other, traditional search, has standard multioption user interface. Results Using a comprehensive set of tasks with 20 volunteers, we found that the Web search interface met data discovery needs and expectations better than the traditional search. A task × interface repeated measures analysis showed a main effect indicating that answers found through the Web search interface were more likely to be correct (F 1,19=37.3, P<.001), with a main effect of task (F 3,57=6.3, P<.001). Further, participants completed the task significantly faster using the Web search interface (F 1,19=18.0, P<.001). There was also a main effect of task (F 2,38=4.1, P=.025, Greenhouse-Geisser correction applied). Overall, participants were asked to rate learnability, ease of use, and satisfaction. Paired mean comparisons showed that the Web search interface received significantly higher ratings than the traditional search interface for learnability (P=.002, 95% CI [0.6-2.4]), ease of use (P<.001, 95% CI [1.2-3.2]), and satisfaction (P<.001, 95% CI [1.8-3.5]). The results show superior cross-domain usability of Web search, which is consistent with its general familiarity and with enabling queries to be refined as the search proceeds, which treats serendipity as part of the refinement. Conclusions The results provide clear evidence that data science should adopt single-field natural language search interfaces for variable search supporting in particular: query reformulation; data browsing; faceted search; surrogates; relevance feedback; summarization, analytics, and visual presentation. PMID:26769334

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

PubMed

Zhang, Junjun; Baran, Joachim; Cros, A; Guberman, Jonathan M; Haider, Syed; Hsu, Jack; Liang, Yong; Rivkin, Elena; Wang, Jianxin; Whitty, Brett; Wong-Erasmus, Marie; Yao, Long; Kasprzyk, Arek

2011-01-01

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources

PubMed Central

Guha, Rajarshi; Nguyen, Dac-Trung; Southall, Noel; Jadhav, Ajit

2012-01-01

Over the last 20 years, there has been an explosion in the amount and type of biological and chemical data that has been made publicly available in a variety of online databases. While this means that vast amounts of information can be found online, there is no guarantee that it can be found easily (or at all). A scientist searching for a specific piece of information is faced with a daunting task - many databases have overlapping content, use their own identifiers and, in some cases, have arcane and unintuitive user interfaces. In this overview, a variety of well known data sources for chemical and biological information are highlighted, focusing on those most useful for chemical biology research. The issue of using multiple data sources together and the associated problems such as identifier disambiguation are highlighted. A brief discussion is then provided on Tripod, a recently developed platform that supports the integration of arbitrary data sources, providing users a simple interface to search across a federated collection of resources. PMID:26609498

UUI: Reusable Spatial Data Services in Unified User Interface at NASA GES DISC

NASA Technical Reports Server (NTRS)

Petrenko, Maksym; Hegde, Mahabaleshwa; Bryant, Keith; Pham, Long B.

2016-01-01

Unified User Interface (UUI) is a next-generation operational data access tool that has been developed at Goddard Earth Sciences Data and Information Services Center(GES DISC) to provide a simple, unified, and intuitive one-stop shop experience for the key data services available at GES DISC, including subsetting (Simple Subset Wizard -SSW), granule file search (Mirador), plotting (Giovanni), and other legacy spatial data services. UUI has been built based on a flexible infrastructure of reusable web services self-contained building blocks that can easily be plugged into spatial applications, including third-party clients or services, to easily enable new functionality as new datasets and services become available. In this presentation, we will discuss our experience in designing UUI services based on open industry standards. We will also explain how the resulting framework can be used for a rapid development, deployment, and integration of spatial data services, facilitating efficient access and dissemination of spatial data sets.

Metadata Creation, Management and Search System for your Scientific Data

NASA Astrophysics Data System (ADS)

Devarakonda, R.; Palanisamy, G.

2012-12-01

Mercury Search Systems is a set of tools for creating, searching, and retrieving of biogeochemical metadata. Mercury toolset provides orders of magnitude improvements in search speed, support for any metadata format, integration with Google Maps for spatial queries, multi-facetted type search, search suggestions, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. Mercury's metadata editor provides a easy way for creating metadata and Mercury's search interface provides a single portal to search for data and information contained in disparate data management systems, each of which may use any metadata format including FGDC, ISO-19115, Dublin-Core, Darwin-Core, DIF, ECHO, and EML. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury is being used more than 14 different projects across 4 federal agencies. It was originally developed for NASA, with continuing development funded by NASA, USGS, and DOE for a consortium of projects. Mercury search won the NASA's Earth Science Data Systems Software Reuse Award in 2008. References: R. Devarakonda, G. Palanisamy, B.E. Wilson, and J.M. Green, "Mercury: reusable metadata management data discovery and access system", Earth Science Informatics, vol. 3, no. 1, pp. 87-94, May 2010. R. Devarakonda, G. Palanisamy, J.M. Green, B.E. Wilson, "Data sharing and retrieval using OAI-PMH", Earth Science Informatics DOI: 10.1007/s12145-010-0073-0, (2010);

Mercury: An Example of Effective Software Reuse for Metadata Management, Data Discovery and Access

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

Devarakonda, Ranjeet

2008-01-01

Mercury is a federated metadata harvesting, data discovery and access tool based on both open source packages and custom developed software. Though originally developed for NASA, the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports the reuse of metadata by enabling searching across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. Mercury provides a single portal to information contained in distributed data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfacesmore » then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. One of the major goals of the recent redesign of Mercury was to improve the software reusability across the 12 projects which currently fund the continuing development of Mercury. These projects span a range of land, atmosphere, and ocean ecological communities and have a number of common needs for metadata searches, but they also have a number of needs specific to one or a few projects. To balance these common and project-specific needs, Mercury's architecture has three major reusable components; a harvester engine, an indexing system and a user interface component. The harvester engine is responsible for harvesting metadata records from various distributed servers around the USA and around the world. The harvester software was packaged in such a way that all the Mercury projects will use the same harvester scripts but each project will be driven by a set of project specific configuration files. The harvested files are structured metadata records that are indexed against the search library API consistently, so that it can render various search capabilities such as simple, fielded, spatial and temporal. This backend component is supported by a very flexible, easy to use Graphical User Interface which is driven by cascading style sheets, which make it even simpler for reusable design implementation. The new Mercury system is based on a Service Oriented Architecture and effectively reuses components for various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. The software also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets, integrated shopping cart to order datasets from various data centers (ORNL DAAC, NSIDC) and integrated visualization tools. Other features include: Filtering and dynamic sorting of search results, book- markable search results, save, retrieve, and modify search criteria.« less

A study of the influence of task familiarity on user behaviors and performance with a MeSH term suggestion interface for PubMed bibliographic search.

PubMed

Tang, Muh-Chyun; Liu, Ying-Hsang; Wu, Wan-Ching

2013-09-01

Previous research has shown that information seekers in biomedical domain need more support in formulating their queries. A user study was conducted to evaluate the effectiveness of a metadata based query suggestion interface for PubMed bibliographic search. The study also investigated the impact of search task familiarity on search behaviors and the effectiveness of the interface. A real user, user search request and real system approach was used for the study. Unlike tradition IR evaluation, where assigned tasks were used, the participants were asked to search requests of their own. Forty-four researchers in Health Sciences participated in the evaluation - each conducted two research requests of their own, alternately with the proposed interface and the PubMed baseline. Several performance criteria were measured to assess the potential benefits of the experimental interface, including users' assessment of their original and eventual queries, the perceived usefulness of the interfaces, satisfaction with the search results, and the average relevance score of the saved records. The results show that, when searching for an unfamiliar topic, users were more likely to change their queries, indicating the effect of familiarity on search behaviors. The results also show that the interface scored higher on several of the performance criteria, such as the "goodness" of the queries, perceived usefulness, and user satisfaction. Furthermore, in line with our hypothesis, the proposed interface was relatively more effective when less familiar search requests were attempted. Results indicate that there is a selective compatibility between search familiarity and search interface. One implication of the research for system evaluation is the importance of taking into consideration task familiarity when assessing the effectiveness of interactive IR systems. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

OceanVideoLab: A Tool for Exploring Underwater Video

NASA Astrophysics Data System (ADS)

Ferrini, V. L.; Morton, J. J.; Wiener, C.

2016-02-01

Video imagery acquired with underwater vehicles is an essential tool for characterizing seafloor ecosystems and seafloor geology. It is a fundamental component of ocean exploration that facilitates real-time operations, augments multidisciplinary scientific research, and holds tremendous potential for public outreach and engagement. Acquiring, documenting, managing, preserving and providing access to large volumes of video acquired with underwater vehicles presents a variety of data stewardship challenges to the oceanographic community. As a result, only a fraction of underwater video content collected with research submersibles is documented, discoverable and/or viewable online. With more than 1 billion users, YouTube offers infrastructure that can be leveraged to help address some of the challenges associated with sharing underwater video with a broad global audience. Anyone can post content to YouTube, and some oceanographic organizations, such as the Schmidt Ocean Institute, have begun live-streaming video directly from underwater vehicles. OceanVideoLab (oceanvideolab.org) was developed to help improve access to underwater video through simple annotation, browse functionality, and integration with related environmental data. Any underwater video that is publicly accessible on YouTube can be registered with OceanVideoLab by simply providing a URL. It is strongly recommended that a navigational file also be supplied to enable geo-referencing of observations. Once a video is registered, it can be viewed and annotated using a simple user interface that integrates observations with vehicle navigation data if provided. This interface includes an interactive map and a list of previous annotations that allows users to jump to times of specific observations in the video. Future enhancements to OceanVideoLab will include the deployment of a search interface, the development of an application program interface (API) that will drive the search and enable querying of content by other systems/tools, the integration of related environmental data from complementary data systems (e.g. temperature, bathymetry), and the expansion of infrastructure to enable broad crowdsourcing of annotations.

Improvements to the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Tauxe, L.; Koppers, A. A. P.; Constable, C.; Jonestrask, L.

2015-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of data uploading and editing, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Online data editing is now available and the need for proprietary spreadsheet software is therefore entirely negated. The data owner can change values in the database or delete entries through an HTML 5 web interface that resembles typical spreadsheets in behavior and uses. Additive uploading now allows for additions to data sets to be uploaded with a simple drag and drop interface. Searching the database has improved with the addition of more sophisticated search parameters and with the facility to use them in complex combinations. A comprehensive summary view of a search result has been added for increased quick data comprehension while a raw data view is available if one desires to see all data columns as stored in the database. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. MagIC data associated with individual contributions or from online searches may be downloaded in the tab delimited MagIC text file format for susbsequent offline use and analysis. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

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.

Seqcrawler: biological data indexing and browsing platform.

PubMed

Sallou, Olivier; Bretaudeau, Anthony; Roult, Aurelien

2012-07-24

Seqcrawler takes its roots in software like SRS or Lucegene. It provides an indexing platform to ease the search of data and meta-data in biological banks and it can scale to face the current flow of data. While many biological bank search tools are available on the Internet, mainly provided by large organizations to search their data, there is a lack of free and open source solutions to browse one's own set of data with a flexible query system and able to scale from a single computer to a cloud system. A personal index platform will help labs and bioinformaticians to search their meta-data but also to build a larger information system with custom subsets of data. The software is scalable from a single computer to a cloud-based infrastructure. It has been successfully tested in a private cloud with 3 index shards (pieces of index) hosting ~400 millions of sequence information (whole GenBank, UniProt, PDB and others) for a total size of 600 GB in a fault tolerant architecture (high-availability). It has also been successfully integrated with software to add extra meta-data from blast results to enhance users' result analysis. Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface. All components (search engine, visualization and data storage), though independent, share a common and coherent data system that can be queried with a simple HTTP interface. The solution scales easily and can also provide a high availability infrastructure.

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

Humphrey, Walter R.

CMS is a Windows application for tracking chemical inventories. Partners will use this application to record chemicals that are stored on their site and to perform periodic inventories of those chemicals. The application records information about stored chemicals from user input via the keyboard and barcode readers and stores that information into a single-file database (SQLite). A simple user login mechanism is used to control access to functions in the application. A user interface is provided that allows users to search the database and update data in the database.

A Graph Approach to Mining Biological Patterns in the Binding Interfaces.

PubMed

Cheng, Wen; Yan, Changhui

2017-01-01

Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, we present a graph-mining method for discovering biological patterns in the protein-RNA interfaces. We represented known protein-RNA interfaces using graphs and then discovered graph patterns enriched in the interfaces. Comparison of the discovered graph patterns with UniProt annotations showed that the graph patterns had a significant overlap with residue sites that had been proven crucial for the RNA binding by experimental methods. Using 200 patterns as input features, a support vector machine method was able to classify protein surface patches into RNA-binding sites and non-RNA-binding sites with 84.0% accuracy and 88.9% precision. We built a simple scoring function that calculated the total number of the graph patterns that occurred in a protein-RNA interface. That scoring function was able to discriminate near-native protein-RNA complexes from docking decoys with a performance comparable with that of a state-of-the-art complex scoring function. Our work also revealed possible patterns that might be important for binding affinity.

The Brazilian Portuguese Lexicon: An Instrument for Psycholinguistic Research

PubMed Central

Estivalet, Gustavo L.; Meunier, Fanny

2015-01-01

In this article, we present the Brazilian Portuguese Lexicon, a new word-based corpus for psycholinguistic and computational linguistic research in Brazilian Portuguese. We describe the corpus development, the specific characteristics on the internet site and database for user access. We also perform distributional analyses of the corpus and comparisons to other current databases. Our main objective was to provide a large, reliable, and useful word-based corpus with a dynamic, easy-to-use, and intuitive interface with free internet access for word and word-criteria searches. We used the Núcleo Interinstitucional de Linguística Computacional’s corpus as the basic data source and developed the Brazilian Portuguese Lexicon by deriving and adding metalinguistic and psycholinguistic information about Brazilian Portuguese words. We obtained a final corpus with more than 30 million word tokens, 215 thousand word types and 25 categories of information about each word. This corpus was made available on the internet via a free-access site with two search engines: a simple search and a complex search. The simple engine basically searches for a list of words, while the complex engine accepts all types of criteria in the corpus categories. The output result presents all entries found in the corpus with the criteria specified in the input search and can be downloaded as a.csv file. We created a module in the results that delivers basic statistics about each search. The Brazilian Portuguese Lexicon also provides a pseudoword engine and specific tools for linguistic and statistical analysis. Therefore, the Brazilian Portuguese Lexicon is a convenient instrument for stimulus search, selection, control, and manipulation in psycholinguistic experiments, as also it is a powerful database for computational linguistics research and language modeling related to lexicon distribution, functioning, and behavior. PMID:26630138

The Brazilian Portuguese Lexicon: An Instrument for Psycholinguistic Research.

PubMed

Estivalet, Gustavo L; Meunier, Fanny

2015-01-01

In this article, we present the Brazilian Portuguese Lexicon, a new word-based corpus for psycholinguistic and computational linguistic research in Brazilian Portuguese. We describe the corpus development, the specific characteristics on the internet site and database for user access. We also perform distributional analyses of the corpus and comparisons to other current databases. Our main objective was to provide a large, reliable, and useful word-based corpus with a dynamic, easy-to-use, and intuitive interface with free internet access for word and word-criteria searches. We used the Núcleo Interinstitucional de Linguística Computacional's corpus as the basic data source and developed the Brazilian Portuguese Lexicon by deriving and adding metalinguistic and psycholinguistic information about Brazilian Portuguese words. We obtained a final corpus with more than 30 million word tokens, 215 thousand word types and 25 categories of information about each word. This corpus was made available on the internet via a free-access site with two search engines: a simple search and a complex search. The simple engine basically searches for a list of words, while the complex engine accepts all types of criteria in the corpus categories. The output result presents all entries found in the corpus with the criteria specified in the input search and can be downloaded as a.csv file. We created a module in the results that delivers basic statistics about each search. The Brazilian Portuguese Lexicon also provides a pseudoword engine and specific tools for linguistic and statistical analysis. Therefore, the Brazilian Portuguese Lexicon is a convenient instrument for stimulus search, selection, control, and manipulation in psycholinguistic experiments, as also it is a powerful database for computational linguistics research and language modeling related to lexicon distribution, functioning, and behavior.

What Searches Do Users Run on PEDro? An Analysis of 893,971 Search Commands Over a 6-Month Period.

PubMed

Stevens, Matthew L; Moseley, Anne; Elkins, Mark R; Lin, Christine C-W; Maher, Chris G

2016-08-05

Clinicians must be able to search effectively for relevant research if they are to provide evidence-based healthcare. It is therefore relevant to consider how users search databases of evidence in healthcare, including what information users look for and what search strategies they employ. To date such analyses have been restricted to the PubMed database. Although the Physiotherapy Evidence Database (PEDro) is searched millions of times each year, no studies have investigated how users search PEDro. To assess the content and quality of searches conducted on PEDro. Searches conducted on the PEDro website over 6 months were downloaded and the 'get' commands and page-views extracted. The following data were tabulated: the 25 most common searches; the number of search terms used; the frequency of use of simple and advanced searches, including the use of each advanced search field; and the frequency of use of various search strategies. Between August 2014 and January 2015, 893,971 search commands were entered on PEDro. Fewer than 18 % of these searches used the advanced search features of PEDro. 'Musculoskeletal' was the most common subdiscipline searched, while 'low back pain' was the most common individual search. Around 20 % of all searches contained errors. PEDro is a commonly used evidence resource, but searching appears to be sub-optimal in many cases. The effectiveness of searches conducted by users needs to improve, which could be facilitated by methods such as targeted training and amending the search interface.

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

Exploring FlyBase Data Using QuickSearch.

PubMed

Marygold, Steven J; Antonazzo, Giulia; Attrill, Helen; Costa, Marta; Crosby, Madeline A; Dos Santos, Gilberto; Goodman, Joshua L; Gramates, L Sian; Matthews, Beverley B; Rey, Alix J; Thurmond, Jim

2016-12-08

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

The NOAA OneStop System: From Well-Curated Metadata to Data Discovery

NASA Astrophysics Data System (ADS)

McQuinn, E.; Jakositz, A.; Caldwell, A.; Delk, Z.; Neufeld, D.; Shapiro, J.; Partee, R.; Milan, A.

2017-12-01

The NOAA OneStop project is a pathfinder in the realm of enabling users to search for, discover, and access NOAA data. As the project continues along its path to maturity, it has become evident that three areas are of utmost importance to its success in the Earth science community: ensuring quality metadata, building a robust and scalable backend architecture, and keeping the user interface simple to use. Why is this the case? Because, simply put, we are dealing with all aspects of a Big Data problem: large volumes of disparate data needing to be quickly and easily processed and retrieved. In this presentation we discuss the three key aspects of OneStop architecture and how development in each area must be done through cross-team collaboration in order to succeed. We cover aspects of the web-based user interface and OneStop API and how metadata curators and software engineers have worked together to continually iterate on an ever-improving data discovery tool meant to be used by a variety of users searching across a broad assortment of data types.

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

Environmental Information Management For Data Discovery and Access System

NASA Astrophysics Data System (ADS)

Giriprakash, P.

2011-01-01

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source software and software developed at Oak Ridge National Laboratory. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. A major new version of Mercury was developed during 2007 and released in early 2008. This new version provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, support for RSS delivery of search results, and ready customization to meet the needs of the multiple projects which use Mercury. For the end users, Mercury provides a single portal to very quickly search for data and information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow ! the users to perform simple, fielded, spatial and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data.

Modeling Search Behaviors during the Acquisition of Expertise in a Sequential Decision-Making Task.

PubMed

Moënne-Loccoz, Cristóbal; Vergara, Rodrigo C; López, Vladimir; Mery, Domingo; Cosmelli, Diego

2017-01-01

Our daily interaction with the world is plagued of situations in which we develop expertise through self-motivated repetition of the same task. In many of these interactions, and especially when dealing with computer and machine interfaces, we must deal with sequences of decisions and actions. For instance, when drawing cash from an ATM machine, choices are presented in a step-by-step fashion and a specific sequence of choices must be performed in order to produce the expected outcome. But, as we become experts in the use of such interfaces, is it possible to identify specific search and learning strategies? And if so, can we use this information to predict future actions? In addition to better understanding the cognitive processes underlying sequential decision making, this could allow building adaptive interfaces that can facilitate interaction at different moments of the learning curve. Here we tackle the question of modeling sequential decision-making behavior in a simple human-computer interface that instantiates a 4-level binary decision tree (BDT) task. We record behavioral data from voluntary participants while they attempt to solve the task. Using a Hidden Markov Model-based approach that capitalizes on the hierarchical structure of behavior, we then model their performance during the interaction. Our results show that partitioning the problem space into a small set of hierarchically related stereotyped strategies can potentially capture a host of individual decision making policies. This allows us to follow how participants learn and develop expertise in the use of the interface. Moreover, using a Mixture of Experts based on these stereotyped strategies, the model is able to predict the behavior of participants that master the task.

The User Interface: How Does Your Product Look and Feel?

ERIC Educational Resources Information Center

Strukhoff, Roger

1987-01-01

Discusses the importance of user cordial interfaces to the successful marketing of optical data disk products, and describes features of several online systems. The topics discussed include full text searching, indexed searching, menu driven interfaces, natural language interfaces, computer graphics, and possible future developments. (CLB)

Design of efficient and simple interface testing equipment for opto-electric tracking system

NASA Astrophysics Data System (ADS)

Liu, Qiong; Deng, Chao; Tian, Jing; Mao, Yao

2016-10-01

Interface testing for opto-electric tracking system is one important work to assure system running performance, aiming to verify the design result of every electronic interface matching the communication protocols or not, by different levels. Opto-electric tracking system nowadays is more complicated, composed of many functional units. Usually, interface testing is executed between units manufactured completely, highly depending on unit design and manufacture progress as well as relative people. As a result, it always takes days or weeks, inefficiently. To solve the problem, this paper promotes an efficient and simple interface testing equipment for opto-electric tracking system, consisting of optional interface circuit card, processor and test program. The hardware cards provide matched hardware interface(s), easily offered from hardware engineer. Automatic code generation technique is imported, providing adaption to new communication protocols. Automatic acquiring items, automatic constructing code architecture and automatic encoding are used to form a new program quickly with adaption. After simple steps, a standard customized new interface testing equipment with matching test program and interface(s) is ready for a waiting-test system in minutes. The efficient and simple interface testing equipment for opto-electric tracking system has worked for many opto-electric tracking system to test entire or part interfaces, reducing test time from days to hours, greatly improving test efficiency, with high software quality and stability, without manual coding. Used as a common tool, the efficient and simple interface testing equipment for opto-electric tracking system promoted by this paper has changed traditional interface testing method and created much higher efficiency.

Evaluation of a Novel Conjunctive Exploratory Navigation Interface for Consumer Health Information: A Crowdsourced Comparative Study

PubMed Central

Cui, Licong; Carter, Rebecca

2014-01-01

Background Numerous consumer health information websites have been developed to provide consumers access to health information. However, lookup search is insufficient for consumers to take full advantage of these rich public information resources. Exploratory search is considered a promising complementary mechanism, but its efficacy has never before been rigorously evaluated for consumer health information retrieval interfaces. Objective This study aims to (1) introduce a novel Conjunctive Exploratory Navigation Interface (CENI) for supporting effective consumer health information retrieval and navigation, and (2) evaluate the effectiveness of CENI through a search-interface comparative evaluation using crowdsourcing with Amazon Mechanical Turk (AMT). Methods We collected over 60,000 consumer health questions from NetWellness, one of the first consumer health websites to provide high-quality health information. We designed and developed a novel conjunctive exploratory navigation interface to explore NetWellness health questions with health topics as dynamic and searchable menus. To investigate the effectiveness of CENI, we developed a second interface with keyword-based search only. A crowdsourcing comparative study was carefully designed to compare three search modes of interest: (A) the topic-navigation-based CENI, (B) the keyword-based lookup interface, and (C) either the most commonly available lookup search interface with Google, or the resident advanced search offered by NetWellness. To compare the effectiveness of the three search modes, 9 search tasks were designed with relevant health questions from NetWellness. Each task included a rating of difficulty level and questions for validating the quality of answers. Ninety anonymous and unique AMT workers were recruited as participants. Results Repeated-measures ANOVA analysis of the data showed the search modes A, B, and C had statistically significant differences among their levels of difficulty (P<.001). Wilcoxon signed-rank test (one-tailed) between A and B showed that A was significantly easier than B (P<.001). Paired t tests (one-tailed) between A and C showed A was significantly easier than C (P<.001). Participant responses on the preferred search modes showed that 47.8% (43/90) participants preferred A, 25.6% (23/90) preferred B, 24.4% (22/90) preferred C. Participant comments on the preferred search modes indicated that CENI was easy to use, provided better organization of health questions by topics, allowed users to narrow down to the most relevant contents quickly, and supported the exploratory navigation by non-experts or those unsure how to initiate their search. Conclusions We presented a novel conjunctive exploratory navigation interface for consumer health information retrieval and navigation. Crowdsourcing permitted a carefully designed comparative search-interface evaluation to be completed in a timely and cost-effective manner with a relatively large number of participants recruited anonymously. Accounting for possible biases, our study has shown for the first time with crowdsourcing that the combination of exploratory navigation and lookup search is more effective than lookup search alone. PMID:24513593

Evaluation of a novel Conjunctive Exploratory Navigation Interface for consumer health information: a crowdsourced comparative study.

PubMed

Cui, Licong; Carter, Rebecca; Zhang, Guo-Qiang

2014-02-10

Numerous consumer health information websites have been developed to provide consumers access to health information. However, lookup search is insufficient for consumers to take full advantage of these rich public information resources. Exploratory search is considered a promising complementary mechanism, but its efficacy has never before been rigorously evaluated for consumer health information retrieval interfaces. This study aims to (1) introduce a novel Conjunctive Exploratory Navigation Interface (CENI) for supporting effective consumer health information retrieval and navigation, and (2) evaluate the effectiveness of CENI through a search-interface comparative evaluation using crowdsourcing with Amazon Mechanical Turk (AMT). We collected over 60,000 consumer health questions from NetWellness, one of the first consumer health websites to provide high-quality health information. We designed and developed a novel conjunctive exploratory navigation interface to explore NetWellness health questions with health topics as dynamic and searchable menus. To investigate the effectiveness of CENI, we developed a second interface with keyword-based search only. A crowdsourcing comparative study was carefully designed to compare three search modes of interest: (A) the topic-navigation-based CENI, (B) the keyword-based lookup interface, and (C) either the most commonly available lookup search interface with Google, or the resident advanced search offered by NetWellness. To compare the effectiveness of the three search modes, 9 search tasks were designed with relevant health questions from NetWellness. Each task included a rating of difficulty level and questions for validating the quality of answers. Ninety anonymous and unique AMT workers were recruited as participants. Repeated-measures ANOVA analysis of the data showed the search modes A, B, and C had statistically significant differences among their levels of difficulty (P<.001). Wilcoxon signed-rank test (one-tailed) between A and B showed that A was significantly easier than B (P<.001). Paired t tests (one-tailed) between A and C showed A was significantly easier than C (P<.001). Participant responses on the preferred search modes showed that 47.8% (43/90) participants preferred A, 25.6% (23/90) preferred B, 24.4% (22/90) preferred C. Participant comments on the preferred search modes indicated that CENI was easy to use, provided better organization of health questions by topics, allowed users to narrow down to the most relevant contents quickly, and supported the exploratory navigation by non-experts or those unsure how to initiate their search. We presented a novel conjunctive exploratory navigation interface for consumer health information retrieval and navigation. Crowdsourcing permitted a carefully designed comparative search-interface evaluation to be completed in a timely and cost-effective manner with a relatively large number of participants recruited anonymously. Accounting for possible biases, our study has shown for the first time with crowdsourcing that the combination of exploratory navigation and lookup search is more effective than lookup search alone.

Surging Seas Risk Finder: A Simple Search-Based Web Tool for Local Sea Level Rise Projections, Coastal Flood Risk Forecasts, and Inundation Exposure Analysis

NASA Astrophysics Data System (ADS)

Strauss, B.; Dodson, D.; Kulp, S. A.; Rizza, D. H.

2016-12-01

Surging Seas Risk Finder (riskfinder.org) is an online tool for accessing extensive local projections and analysis of sea level rise; coastal floods; and land, populations, contamination sources, and infrastructure and other assets that may be exposed to inundation. Risk Finder was first published in 2013 for Florida, New York and New Jersey, expanding to all states in the contiguous U.S. by 2016, when a major new version of the tool was released with a completely new interface. The revised tool was informed by hundreds of survey responses from and conversations with planners, local officials and other coastal stakeholders, plus consideration of modern best practices for responsive web design and user interfaces, and social science-based principles for science communication. Overarching design principles include simplicity and ease of navigation, leading to a landing page with Google-like sparsity and focus on search, and to an architecture based on search, so that each coastal zip code, city, county, state or other place type has its own webpage gathering all relevant analysis in modular, scrollable units. Millions of users have visited the Surging Seas suite of tools to date, and downloaded thousands of files, for stated purposes ranging from planning to business to education to personal decisions; and from institutions ranging from local to federal government agencies, to businesses, to NGOs, and to academia.

Knowledge acquisition for case-based reasoning systems

NASA Technical Reports Server (NTRS)

Riesbeck, Christopher K.

1988-01-01

Case-based reasoning (CBR) is a simple idea: solve new problems by adapting old solutions to similar problems. The CBR approach offers several potential advantages over rule-based reasoning: rules are not combined blindly in a search for solutions, solutions can be explained in terms of concrete examples, and performance can improve automatically as new problems are solved and added to the case library. Moving CBR for the university research environment to the real world requires smooth interfaces for getting knowledge from experts. Described are the basic elements of an interface for acquiring three basic bodies of knowledge that any case-based reasoner requires: the case library of problems and their solutions, the analysis rules that flesh out input problem specifications so that relevant cases can be retrieved, and the adaptation rules that adjust old solutions to fit new problems.

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…

One Click to the Cosmos: The AstroPix Image Archive

NASA Astrophysics Data System (ADS)

Hurt, Robert L.; Llamas, J.; Squires, G. K.; Brinkworth, C.; X-ray Center, Chandra; ESO/ESA; Science Center, Spitzer; STScI

2013-01-01

Imagine a single website that acts as a portal to the entire wealth of public imagery spanning the world's observatories. This is the goal of the AstroPix project (astropix.ipac.caltech.edu), and you can use it today! Although still in a beta development state, this past year has seen the inclusion of thousands of images spanning some of the most prominent observatories in the world, including Chandra, ESO, Galex, Herschel, Hubble, Spitzer, and WISE, with more on the way. The archive is unique as it is built around the Astronomical Visualization Metadata (AVM) standard, which captures the rich contextual information for each image. This ranges from titles and descriptions, to color representations and observation details, to sky coordinates. AVM enables AstroPix imagery to be used in a variety of unique ways that benefit formal and informal education as well as astronomers and the general public. Visitors to Astropix can search the database using simple free-text queries, or use a structured search (similar to "Smart Playlists" found in iTunes, for example). We are also developing public application programming interfaces (APIs) to allow third party software and websites to access the growing content for a variety of uses (planetarium software, museum kiosks, mobile apps, and creative web interfaces, to name a few). Contributing image assets to AstroPix is as easy as tagging the images with the relevant metadata and including the web links to the images in a simple RSS feed. We will cover some of the latest information about tools to contribute images to AstroPix and ways to use the site.

Mercury- Distributed Metadata Management, Data Discovery and Access System

NASA Astrophysics Data System (ADS)

Palanisamy, Giri; Wilson, Bruce E.; Devarakonda, Ranjeet; Green, James M.

2007-12-01

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source and ORNL- developed software. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports various metadata standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115 (under development). Mercury provides a single portal to information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury supports various projects including: ORNL DAAC, NBII, DADDI, LBA, NARSTO, CDIAC, OCEAN, I3N, IAI, ESIP and ARM. The new Mercury system is based on a Service Oriented Architecture and supports various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. This system also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets. Other features include: Filtering and dynamic sorting of search results, book-markable search results, save, retrieve, and modify search criteria.

Finding and Exploring Health Information with a Slider-Based User Interface.

PubMed

Pang, Patrick Cheong-Iao; Verspoor, Karin; Pearce, Jon; Chang, Shanton

2016-01-01

Despite the fact that search engines are the primary channel to access online health information, there are better ways to find and explore health information on the web. Search engines are prone to problems when they are used to find health information. For instance, users have difficulties in expressing health scenarios with appropriate search keywords, search results are not optimised for medical queries, and the search process does not account for users' literacy levels and reading preferences. In this paper, we describe our approach to addressing these problems by introducing a novel design using a slider-based user interface for discovering health information without the need for precise search keywords. The user evaluation suggests that the interface is easy to use and able to assist users in the process of discovering new information. This study demonstrates the potential value of adopting slider controls in the user interface of health websites for navigation and information discovery.

CellLineNavigator: a workbench for cancer cell line analysis

PubMed Central

Krupp, Markus; Itzel, Timo; Maass, Thorsten; Hildebrandt, Andreas; Galle, Peter R.; Teufel, Andreas

2013-01-01

The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search ability, a simple data and an intuitive querying interface were implemented. It allows the user to explore and filter gene expression, focusing on pathological or physiological conditions. For a more complex search, the advanced query interface may be used to query for (i) differentially expressed genes; (ii) pathological or physiological conditions; or (iii) gene names or functional attributes, such as Kyoto Encyclopaedia of Genes and Genomes pathway maps. These queries may also be combined. Finally, CellLineNavigator allows additional advanced analysis of differentially regulated genes by a direct link to the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources. PMID:23118487

Earthdata Search Summer ESIP Usability Workshop

NASA Technical Reports Server (NTRS)

Reese, Mark; Sirato, Jeff

2017-01-01

The Earthdata Search Client has undergone multiple rounds of usability testing during 2017 and the user feedback received has resulted in an enhanced user interface. This session will showcase the new Earthdata Search Client user interface and provide hands-on experience for participants to learn how to search, visualize and download data in the desired format.

Does linear separability really matter? Complex visual search is explained by simple search

PubMed Central

Vighneshvel, T.; Arun, S. P.

2013-01-01

Visual search in real life involves complex displays with a target among multiple types of distracters, but in the laboratory, it is often tested using simple displays with identical distracters. Can complex search be understood in terms of simple searches? This link may not be straightforward if complex search has emergent properties. One such property is linear separability, whereby search is hard when a target cannot be separated from its distracters using a single linear boundary. However, evidence in favor of linear separability is based on testing stimulus configurations in an external parametric space that need not be related to their true perceptual representation. We therefore set out to assess whether linear separability influences complex search at all. Our null hypothesis was that complex search performance depends only on classical factors such as target-distracter similarity and distracter homogeneity, which we measured using simple searches. Across three experiments involving a variety of artificial and natural objects, differences between linearly separable and nonseparable searches were explained using target-distracter similarity and distracter heterogeneity. Further, simple searches accurately predicted complex search regardless of linear separability (r = 0.91). Our results show that complex search is explained by simple search, refuting the widely held belief that linear separability influences visual search. PMID:24029822

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

PubMed Central

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry BF; Tipton, Keith F

2007-01-01

Background We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. Description The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at . The data are available for download as SQL and XML files via FTP. Conclusion ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List. PMID:17662133

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

PubMed

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

Querying Event Sequences by Exact Match or Similarity Search: Design and Empirical Evaluation

PubMed Central

Wongsuphasawat, Krist; Plaisant, Catherine; Taieb-Maimon, Meirav; Shneiderman, Ben

2012-01-01

Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both. PMID:22379286

Informedia at TRECVID 2003: Analyzing and Searching Broadcast News Video

DTIC Science & Technology

2004-11-03

browsing interface to browse the top-ranked shots according to the different classifiers. Color and texture based image search engines were also...different classifiers. Color and texture based image search engines were also optimized better performance. This “new” interface was evaluated as

The new Planetary Science Archive: A tool for exploration and discovery of scientific datasets from ESA's planetary missions

NASA Astrophysics Data System (ADS)

Heather, David

2016-07-01

Introduction: The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces (e.g. FTP browser, Map based, Advanced search, and Machine interface): http://archives.esac.esa.int/psa All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. Updating the PSA: The PSA is currently implementing a number of significant changes, both to its web-based interface to the scientific community, and to its database structure. The new PSA will be up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's upcoming ExoMars and BepiColombo missions. The newly designed PSA homepage will provide direct access to scientific datasets via a text search for targets or missions. This will significantly reduce the complexity for users to find their data and will promote one-click access to the datasets. Additionally, the homepage will provide direct access to advanced views and searches of the datasets. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). Queries to the PSA database will be possible either via the homepage (for simple searches of missions or targets), or through a filter menu for more tailored queries. The filter menu will offer multiple options to search for a particular dataset or product, and will manage queries for both in-situ and remote sensing instruments. Parameters such as start-time, phase angle, and heliocentric distance will be emphasized. A further advanced search function will allow users to query all the metadata present in the PSA database. Results will be displayed in 3 different ways: 1) A table listing all the corresponding data matching the criteria in the filter menu, 2) a projection of the products onto the surface of the object when applicable (i.e. planets, small bodies), and 3) a list of images for the relevant instruments to enjoy the beauty of our Solar System. These different ways of viewing the datasets will ensure that scientists and non-professionals alike will have access to the specific data they are looking for, regardless of their background. Conclusions: The new PSA will maintain the various interfaces and services it had in the past, and will include significant improvements designed to allow easier and more effective access to the scientific data and supporting materials. The new PSA is expected to be released by mid-2016. It will support the past, present and future missions, ancillary datasets, and will enhance the scientific output of ESA's missions. As such, the PSA will become a unique archive ensuring the long-term preservation and usage of scientific datasets together with user-friendly access.

The new Planetary Science Archive: A tool for exploration and discovery of scientific datasets from ESA's planetary missions.

NASA Astrophysics Data System (ADS)

Heather, David; Besse, Sebastien; Barbarisi, Isa; Arviset, Christophe; de Marchi, Guido; Barthelemy, Maud; Docasal, Ruben; Fraga, Diego; Grotheer, Emmanuel; Lim, Tanya; Macfarlane, Alan; Martinez, Santa; Rios, Carlos

2016-04-01

Introduction: The Planetary Science Archive (PSA) is the European Space Agency's (ESA) repository of science data from all planetary science and exploration missions. The PSA provides access to scientific datasets through various interfaces (e.g. FTP browser, Map based, Advanced search, and Machine interface): http://archives.esac.esa.int/psa All datasets are scientifically peer-reviewed by independent scientists, and are compliant with the Planetary Data System (PDS) standards. Updating the PSA: The PSA is currently implementing a number of significant changes, both to its web-based interface to the scientific community, and to its database structure. The new PSA will be up-to-date with versions 3 and 4 of the PDS standards, as PDS4 will be used for ESA's upcoming ExoMars and BepiColombo missions. The newly designed PSA homepage will provide direct access to scientific datasets via a text search for targets or missions. This will significantly reduce the complexity for users to find their data and will promote one-click access to the datasets. Additionally, the homepage will provide direct access to advanced views and searches of the datasets. Users will have direct access to documentation, information and tools that are relevant to the scientific use of the dataset, including ancillary datasets, Software Interface Specification (SIS) documents, and any tools/help that the PSA team can provide. A login mechanism will provide additional functionalities to the users to aid / ease their searches (e.g. saving queries, managing default views). Queries to the PSA database will be possible either via the homepage (for simple searches of missions or targets), or through a filter menu for more tailored queries. The filter menu will offer multiple options to search for a particular dataset or product, and will manage queries for both in-situ and remote sensing instruments. Parameters such as start-time, phase angle, and heliocentric distance will be emphasized. A further advanced search function will allow users to query all the metadata present in the PSA database. Results will be displayed in 3 different ways: 1) A table listing all the corresponding data matching the criteria in the filter menu, 2) a projection of the products onto the surface of the object when applicable (i.e. planets, small bodies), and 3) a list of images for the relevant instruments to enjoy the beauty of our Solar System. These different ways of viewing the datasets will ensure that scientists and non-professionals alike will have access to the specific data they are looking for, regardless of their background. Conclusions: The new PSA will maintain the various interfaces and services it had in the past, and will include significant improvements designed to allow easier and more effective access to the scientific data and supporting materials. The new PSA is expected to be released by mid-2016. It will support the past, present and future missions, ancillary datasets, and will enhance the scientific output of ESA's missions. As such, the PSA will become a unique archive ensuring the long-term preservation and usage of scientific datasets together with user-friendly access.

What a Difference a Tag Cloud Makes: Effects of Tasks and Cognitive Abilities on Search Results Interface Use

ERIC Educational Resources Information Center

Gwizdka, Jacek

2009-01-01

Introduction: The goal of this study is to expand our understanding of the relationships between selected tasks, cognitive abilities and search result interfaces. The underlying objective is to understand how to select search results presentation for tasks and user contexts Method: Twenty three participants conducted four search tasks of two types…

The effect of four user interface concepts on visual scan pattern similarity and information foraging in a complex decision making task.

PubMed

Starke, Sandra D; Baber, Chris

2018-07-01

User interface (UI) design can affect the quality of decision making, where decisions based on digitally presented content are commonly informed by visually sampling information through eye movements. Analysis of the resulting scan patterns - the order in which people visually attend to different regions of interest (ROIs) - gives an insight into information foraging strategies. In this study, we quantified scan pattern characteristics for participants engaging with conceptually different user interface designs. Four interfaces were modified along two dimensions relating to effort in accessing information: data presentation (either alpha-numerical data or colour blocks), and information access time (all information sources readily available or sequential revealing of information required). The aim of the study was to investigate whether a) people develop repeatable scan patterns and b) different UI concepts affect information foraging and task performance. Thirty-two participants (eight for each UI concept) were given the task to correctly classify 100 credit card transactions as normal or fraudulent based on nine transaction attributes. Attributes varied in their usefulness of predicting the correct outcome. Conventional and more recent (network analysis- and bioinformatics-based) eye tracking metrics were used to quantify visual search. Empirical findings were evaluated in context of random data and possible accuracy for theoretical decision making strategies. Results showed short repeating sequence fragments within longer scan patterns across participants and conditions, comprising a systematic and a random search component. The UI design concept showing alpha-numerical data in full view resulted in most complete data foraging, while the design concept showing colour blocks in full view resulted in the fastest task completion time. Decision accuracy was not significantly affected by UI design. Theoretical calculations showed that the difference in achievable accuracy between very complex and simple decision making strategies was small. We conclude that goal-directed search of familiar information results in repeatable scan pattern fragments (often corresponding to information sources considered particularly important), but no repeatable complete scan pattern. The underlying concept of the UI affects how visual search is performed, and a decision making strategy develops. This should be taken in consideration when designing for applied domains. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Design of SimpleITK.

PubMed

Lowekamp, Bradley C; Chen, David T; Ibáñez, Luis; Blezek, Daniel

2013-01-01

SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org.

A Search Engine Features Comparison.

ERIC Educational Resources Information Center

Vorndran, Gerald

Until recently, the World Wide Web (WWW) public access search engines have not included many of the advanced commands, options, and features commonly available with the for-profit online database user interfaces, such as DIALOG. This study evaluates the features and characteristics common to both types of search interfaces, examines the Web search…

A rank-based Prediction Algorithm of Learning User's Intention

NASA Astrophysics Data System (ADS)

Shen, Jie; Gao, Ying; Chen, Cang; Gong, HaiPing

Internet search has become an important part in people's daily life. People can find many types of information to meet different needs through search engines on the Internet. There are two issues for the current search engines: first, the users should predetermine the types of information they want and then change to the appropriate types of search engine interfaces. Second, most search engines can support multiple kinds of search functions, each function has its own separate search interface. While users need different types of information, they must switch between different interfaces. In practice, most queries are corresponding to various types of information results. These queries can search the relevant results in various search engines, such as query "Palace" contains the websites about the introduction of the National Palace Museum, blog, Wikipedia, some pictures and video information. This paper presents a new aggregative algorithm for all kinds of search results. It can filter and sort the search results by learning three aspects about the query words, search results and search history logs to achieve the purpose of detecting user's intention. Experiments demonstrate that this rank-based method for multi-types of search results is effective. It can meet the user's search needs well, enhance user's satisfaction, provide an effective and rational model for optimizing search engines and improve user's search experience.

Forming-free and self-rectifying resistive switching of the simple Pt/TaOx/n-Si structure for access device-free high-density memory application

NASA Astrophysics Data System (ADS)

Gao, Shuang; Zeng, Fei; Li, Fan; Wang, Minjuan; Mao, Haijun; Wang, Guangyue; Song, Cheng; Pan, Feng

2015-03-01

The search for self-rectifying resistive memories has aroused great attention due to their potential in high-density memory applications without additional access devices. Here we report the forming-free and self-rectifying bipolar resistive switching behavior of a simple Pt/TaOx/n-Si tri-layer structure. The forming-free phenomenon is attributed to the generation of a large amount of oxygen vacancies, in a TaOx region that is in close proximity to the TaOx/n-Si interface, via out-diffusion of oxygen ions from TaOx to n-Si. A maximum rectification ratio of ~6 × 102 is obtained when the Pt/TaOx/n-Si devices stay in a low resistance state, which originates from the existence of a Schottky barrier between the formed oxygen vacancy filament and the n-Si electrode. More importantly, numerical simulation reveals that the self-rectifying behavior itself can guarantee a maximum crossbar size of 212 × 212 (~44 kbit) on the premise of 10% read margin. Moreover, satisfactory switching uniformity and retention performance are observed based on this simple tri-layer structure. All of these results demonstrate the great potential of this simple Pt/TaOx/n-Si tri-layer structure for access device-free high-density memory applications.The search for self-rectifying resistive memories has aroused great attention due to their potential in high-density memory applications without additional access devices. Here we report the forming-free and self-rectifying bipolar resistive switching behavior of a simple Pt/TaOx/n-Si tri-layer structure. The forming-free phenomenon is attributed to the generation of a large amount of oxygen vacancies, in a TaOx region that is in close proximity to the TaOx/n-Si interface, via out-diffusion of oxygen ions from TaOx to n-Si. A maximum rectification ratio of ~6 × 102 is obtained when the Pt/TaOx/n-Si devices stay in a low resistance state, which originates from the existence of a Schottky barrier between the formed oxygen vacancy filament and the n-Si electrode. More importantly, numerical simulation reveals that the self-rectifying behavior itself can guarantee a maximum crossbar size of 212 × 212 (~44 kbit) on the premise of 10% read margin. Moreover, satisfactory switching uniformity and retention performance are observed based on this simple tri-layer structure. All of these results demonstrate the great potential of this simple Pt/TaOx/n-Si tri-layer structure for access device-free high-density memory applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr06406b

Spying on Search Strategies

ERIC Educational Resources Information Center

Tenopir, Carol

2004-01-01

Only the most dedicated super-searchers are motivated to learn and control command systems, like DialogClassic, that rely on the user to input complex search strategies. Infrequent searchers and most end users choose interfaces that do some of the work for them and make the search process appear easy. However, the easier a good interface seems to…

Google Scholar as replacement for systematic literature searches: good relative recall and precision are not enough.

PubMed

Boeker, Martin; Vach, Werner; Motschall, Edith

2013-10-26

Recent research indicates a high recall in Google Scholar searches for systematic reviews. These reports raised high expectations of Google Scholar as a unified and easy to use search interface. However, studies on the coverage of Google Scholar rarely used the search interface in a realistic approach but instead merely checked for the existence of gold standard references. In addition, the severe limitations of the Google Search interface must be taken into consideration when comparing with professional literature retrieval tools.The objectives of this work are to measure the relative recall and precision of searches with Google Scholar under conditions which are derived from structured search procedures conventional in scientific literature retrieval; and to provide an overview of current advantages and disadvantages of the Google Scholar search interface in scientific literature retrieval. General and MEDLINE-specific search strategies were retrieved from 14 Cochrane systematic reviews. Cochrane systematic review search strategies were translated to Google Scholar search expression as good as possible under consideration of the original search semantics. The references of the included studies from the Cochrane reviews were checked for their inclusion in the result sets of the Google Scholar searches. Relative recall and precision were calculated. We investigated Cochrane reviews with a number of included references between 11 and 70 with a total of 396 references. The Google Scholar searches resulted in sets between 4,320 and 67,800 and a total of 291,190 hits. The relative recall of the Google Scholar searches had a minimum of 76.2% and a maximum of 100% (7 searches). The precision of the Google Scholar searches had a minimum of 0.05% and a maximum of 0.92%. The overall relative recall for all searches was 92.9%, the overall precision was 0.13%. The reported relative recall must be interpreted with care. It is a quality indicator of Google Scholar confined to an experimental setting which is unavailable in systematic retrieval due to the severe limitations of the Google Scholar search interface. Currently, Google Scholar does not provide necessary elements for systematic scientific literature retrieval such as tools for incremental query optimization, export of a large number of references, a visual search builder or a history function. Google Scholar is not ready as a professional searching tool for tasks where structured retrieval methodology is necessary.

STScI Archive Manual, Version 7.0

NASA Astrophysics Data System (ADS)

Padovani, Paolo

1999-06-01

The STScI Archive Manual provides information a user needs to know to access the HST archive via its two user interfaces: StarView and a World Wide Web (WWW) interface. It provides descriptions of the StarView screens used to access information in the database and the format of that information, and introduces the use to the WWW interface. Using the two interfaces, users can search for observations, preview public data, and retrieve data from the archive. Using StarView one can also find calibration reference files and perform detailed association searches. With the WWW interface archive users can access, and obtain information on, all Multimission Archive at Space Telescope (MAST) data, a collection of mainly optical and ultraviolet datasets which include, amongst others, the International Ultraviolet Explorer (IUE) Final Archive. Both interfaces feature a name resolver which simplifies searches based on target name.

Searching ClinicalTrials.gov and the International Clinical Trials Registry Platform to inform systematic reviews: what are the optimal search approaches?

PubMed

Glanville, Julie M; Duffy, Steven; McCool, Rachael; Varley, Danielle

2014-07-01

Since 2005, International Committee of Medical Journal Editors (ICMJE) member journals have required that clinical trials be registered in publicly available trials registers before they are considered for publication. The research explores whether it is adequate, when searching to inform systematic reviews, to search for relevant clinical trials using only public trials registers and to identify the optimal search approaches in trials registers. A search was conducted in ClinicalTrials.gov and the International Clinical Trials Registry Platform (ICTRP) for research studies that had been included in eight systematic reviews. Four search approaches (highly sensitive, sensitive, precise, and highly precise) were performed using the basic and advanced interfaces in both resources. On average, 84% of studies were not listed in either resource. The largest number of included studies was retrieved in ClinicalTrials.gov and ICTRP when a sensitive search approach was used in the basic interface. The use of the advanced interface maintained or improved sensitivity in 16 of 19 strategies for Clinicaltrials.gov and 8 of 18 for ICTRP. No single search approach was sensitive enough to identify all studies included in the 6 reviews. Trials registers cannot yet be relied upon as the sole means to locate trials for systematic reviews. Trials registers lag behind the major bibliographic databases in terms of their search interfaces. For systematic reviews, trials registers and major bibliographic databases should be searched. Trials registers should be searched using sensitive approaches, and both the registers consulted in this study should be searched.

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

PubMed

Vaudel, Marc; Barsnes, Harald; Berven, Frode S; Sickmann, Albert; Martens, Lennart

2011-03-01

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework.

PubMed

Marenco, Luis; Li, Yuli; Martone, Maryann E; Sternberg, Paul W; Shepherd, Gordon M; Miller, Perry L

2008-09-01

This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface.

Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

PubMed Central

Li, Yuli; Martone, Maryann E.; Sternberg, Paul W.; Shepherd, Gordon M.; Miller, Perry L.

2009-01-01

This paper describes a pilot query interface that has been constructed to help us explore a “concept-based” approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface. PMID:18953674

The Design of SimpleITK

PubMed Central

Lowekamp, Bradley C.; Chen, David T.; Ibáñez, Luis; Blezek, Daniel

2013-01-01

SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org. PMID:24416015

The Phyre2 web portal for protein modelling, prediction and analysis

PubMed Central

Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael JE

2017-01-01

Summary Phyre2 is a suite of tools available on the web to predict and analyse protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a protocol. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyse the effect of amino-acid variants (e.g. nsSNPs) for a user’s protein sequence. Users are guided through results by a simple interface at a level of detail determined by them. This protocol will guide a user from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30mins and 2 hours after submission. PMID:25950237

Patscanui: an intuitive web interface for searching patterns in DNA and protein data.

PubMed

Blin, Kai; Wohlleben, Wolfgang; Weber, Tilmann

2018-05-02

Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolites.org/) provides a highly interactive web interface to the powerful generic pattern search tool PatScan. The complex PatScan-patterns are created in a drag-and-drop aware interface allowing researchers to do rapid prototyping of the often complicated patterns useful to identifying features of interest.

LBT Distributed Archive: Status and Features

NASA Astrophysics Data System (ADS)

Knapic, C.; Smareglia, R.; Thompson, D.; Grede, G.

2011-07-01

After the first release of the LBT Distributed Archive, this successful collaboration is continuing within the LBT corporation. The IA2 (Italian Center for Astronomical Archive) team had updated the LBT DA with new features in order to facilitate user data retrieval while abiding by VO standards. To facilitate the integration of data from any new instruments, we have migrated to a new database, developed new data distribution software, and enhanced features in the LBT User Interface. The DBMS engine has been changed to MySQL. Consequently, the data handling software now uses java thread technology to update and synchronize the main storage archives on Mt. Graham and in Tucson, as well as archives in Trieste and Heidelberg, with all metadata and proprietary data. The LBT UI has been updated with additional features allowing users to search by instrument and some of the more important characteristics of the images. Finally, instead of a simple cone search service over all LBT image data, new instrument specific SIAP and cone search services have been developed. They will be published in the IVOA framework later this fall.

A "Simple Query Interface" Adapter for the Discovery and Exchange of Learning Resources

ERIC Educational Resources Information Center

Massart, David

2006-01-01

Developed as part of CEN/ISSS Workshop on Learning Technology efforts to improve interoperability between learning resource repositories, the Simple Query Interface (SQI) is an Application Program Interface (API) for querying heterogeneous repositories of learning resource metadata. In the context of the ProLearn Network of Excellence, SQI is used…

M"Health" for Higher Education

ERIC Educational Resources Information Center

Aburas, Abdurazzag A.; Ayran, Mujgan

2013-01-01

Better education is required better advanced tools to be used for students. Smart phone becomes main part of our daily life. New medical design interface is introduced for medicine student based mobile. The Graphic User Interface must be easy and simple. The main interface design issue for mobile is simple and easy to use. Human Mobile…

Chapter 11: Web-based Tools - VO Region Inventory Service

NASA Astrophysics Data System (ADS)

Good, J. C.

As the size and number of datasets available through the VO grows, it becomes increasingly critical to have services that aid in locating and characterizing data pertinent to a particular scientific problem. At the same time, this same increase makes that goal more and more difficult to achieve. With a small number of datasets, it is feasible to simply retrieve the data itself (as the NVO DataScope service does). At intermediate scales, "count" DBMS searches (searches of the actual datasets which return record counts rather than full data subsets) sent to each data provider will work. However, neither of these approaches scale as the number of datasets expands into the hundreds or thousands. Dealing with the same problem internally, IRSA developed a compact and extremely fast scheme for determining source counts for positional catalogs (and in some cases image metadata) over arbitrarily large regions for multiple catalogs in a fraction of a second. To show applicability to the VO in general, this service has been extended with indices for all 4000+ catalogs in CDS Vizier (essentially all published catalogs and source tables). In this chapter, we will briefly describe the architecture of this service, and then describe how this can be used in a distributed system to retrieve rapid inventories of all VO holdings in a way that places an insignificant load on any data supplier. Further, we show and this tool can be used in conjunction with VO Registries and catalog services to zero in on those datasets that are appropriate to the user's needs. The initial implementation of this service consolidates custom binary index file structures (external to any DBMS and therefore portable) at a single site to minimize search times and implements the search interface as a simple CGI program. However, the architecture is amenable to distribution. The next phase of development will focus on metadata harvesting from data archives through a standard program interface and distribution of the search processing across multiple service providers for redundancy and parallelization.

Usability evaluation of an experimental text summarization system and three search engines: implications for the reengineering of health care interfaces.

PubMed

Kushniruk, Andre W; Kan, Min-Yem; McKeown, Kathleen; Klavans, Judith; Jordan, Desmond; LaFlamme, Mark; Patel, Vimia L

2002-01-01

This paper describes the comparative evaluation of an experimental automated text summarization system, Centrifuser and three conventional search engines - Google, Yahoo and About.com. Centrifuser provides information to patients and families relevant to their questions about specific health conditions. It then produces a multidocument summary of articles retrieved by a standard search engine, tailored to the user's question. Subjects, consisting of friends or family of hospitalized patients, were asked to "think aloud" as they interacted with the four systems. The evaluation involved audio- and video recording of subject interactions with the interfaces in situ at a hospital. Results of the evaluation show that subjects found Centrifuser's summarization capability useful and easy to understand. In comparing Centrifuser to the three search engines, subjects' ratings varied; however, specific interface features were deemed useful across interfaces. We conclude with a discussion of the implications for engineering Web-based retrieval systems.

Comparative Recall and Precision of Simple and Expert Searches in Google Scholar and Eight Other Databases

ERIC Educational Resources Information Center

Walters, William H.

2011-01-01

This study evaluates the effectiveness of simple and expert searches in Google Scholar (GS), EconLit, GEOBASE, PAIS, POPLINE, PubMed, Social Sciences Citation Index, Social Sciences Full Text, and Sociological Abstracts. It assesses the recall and precision of 32 searches in the field of later-life migration: nine simple keyword searches and 23…

Google Scholar as replacement for systematic literature searches: good relative recall and precision are not enough

PubMed Central

2013-01-01

Background Recent research indicates a high recall in Google Scholar searches for systematic reviews. These reports raised high expectations of Google Scholar as a unified and easy to use search interface. However, studies on the coverage of Google Scholar rarely used the search interface in a realistic approach but instead merely checked for the existence of gold standard references. In addition, the severe limitations of the Google Search interface must be taken into consideration when comparing with professional literature retrieval tools. The objectives of this work are to measure the relative recall and precision of searches with Google Scholar under conditions which are derived from structured search procedures conventional in scientific literature retrieval; and to provide an overview of current advantages and disadvantages of the Google Scholar search interface in scientific literature retrieval. Methods General and MEDLINE-specific search strategies were retrieved from 14 Cochrane systematic reviews. Cochrane systematic review search strategies were translated to Google Scholar search expression as good as possible under consideration of the original search semantics. The references of the included studies from the Cochrane reviews were checked for their inclusion in the result sets of the Google Scholar searches. Relative recall and precision were calculated. Results We investigated Cochrane reviews with a number of included references between 11 and 70 with a total of 396 references. The Google Scholar searches resulted in sets between 4,320 and 67,800 and a total of 291,190 hits. The relative recall of the Google Scholar searches had a minimum of 76.2% and a maximum of 100% (7 searches). The precision of the Google Scholar searches had a minimum of 0.05% and a maximum of 0.92%. The overall relative recall for all searches was 92.9%, the overall precision was 0.13%. Conclusion The reported relative recall must be interpreted with care. It is a quality indicator of Google Scholar confined to an experimental setting which is unavailable in systematic retrieval due to the severe limitations of the Google Scholar search interface. Currently, Google Scholar does not provide necessary elements for systematic scientific literature retrieval such as tools for incremental query optimization, export of a large number of references, a visual search builder or a history function. Google Scholar is not ready as a professional searching tool for tasks where structured retrieval methodology is necessary. PMID:24160679

SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study

PubMed Central

Muin, Michael; Fontelo, Paul; Liu, Fang; Ackerman, Michael

2005-01-01

Background With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. Results Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. Conclusion SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine. PMID:16321145

SLIM: an alternative Web interface for MEDLINE/PubMed searches - a preliminary study.

PubMed

Muin, Michael; Fontelo, Paul; Liu, Fang; Ackerman, Michael

2005-12-01

With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine.

Implementation and application of an interactive user-friendly validation software for RADIANCE

NASA Astrophysics Data System (ADS)

Sundaram, Anand; Boonn, William W.; Kim, Woojin; Cook, Tessa S.

2012-02-01

RADIANCE extracts CT dose parameters from dose sheets using optical character recognition and stores the data in a relational database. To facilitate validation of RADIANCE's performance, a simple user interface was initially implemented and about 300 records were evaluated. Here, we extend this interface to achieve a wider variety of functions and perform a larger-scale validation. The validator uses some data from the RADIANCE database to prepopulate quality-testing fields, such as correspondence between calculated and reported total dose-length product. The interface also displays relevant parameters from the DICOM headers. A total of 5,098 dose sheets were used to test the performance accuracy of RADIANCE in dose data extraction. Several search criteria were implemented. All records were searchable by accession number, study date, or dose parameters beyond chosen thresholds. Validated records were searchable according to additional criteria from validation inputs. An error rate of 0.303% was demonstrated in the validation. Dose monitoring is increasingly important and RADIANCE provides an open-source solution with a high level of accuracy. The RADIANCE validator has been updated to enable users to test the integrity of their installation and verify that their dose monitoring is accurate and effective.

First Prototype of a Web Map Interface for ESA's Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Manaud, N.; Gonzalez, J.

2014-04-01

We present a first prototype of a Web Map Interface that will serve as a proof of concept and design for ESA's future fully web-based Planetary Science Archive (PSA) User Interface. The PSA is ESA's planetary science archiving authority and central repository for all scientific and engineering data returned by ESA's Solar System missions [1]. All data are compliant with NASA's Planetary Data System (PDS) Standards and are accessible through several interfaces [2]: in addition to serving all public data via FTP and the Planetary Data Access Protocol (PDAP), a Java-based User Interface provides advanced search, preview, download, notification and delivery-basket functionality. It allows the user to query and visualise instrument observations footprints using a map-based interface (currently only available for Mars Express HRSC and OMEGA instruments). During the last decade, the planetary mapping science community has increasingly been adopting Geographic Information System (GIS) tools and standards, originally developed for and used in Earth science. There is an ongoing effort to produce and share cartographic products through Open Geospatial Consortium (OGC) Web Services, or as standalone data sets, so that they can be readily used in existing GIS applications [3,4,5]. Previous studies conducted at ESAC [6,7] have helped identify the needs of Planetary GIS users, and define key areas of improvement for the future Web PSA User Interface. Its web map interface shall will provide access to the full geospatial content of the PSA, including (1) observation geometry footprints of all remote sensing instruments, and (2) all georeferenced cartographic products, such as HRSC map-projected data or OMEGA global maps from Mars Express. It shall aim to provide a rich user experience for search and visualisation of this content using modern and interactive web mapping technology. A comprehensive set of built-in context maps from external sources, such as MOLA topography, TES infrared maps or planetary surface nomenclature, provided in both simple cylindrical and polar stereographic projections, shall enhance this user experience. In addition, users should be able to import and export data in commonly used open- GIS formats. It is also intended to serve all PSA geospatial data through OGC-compliant Web Services so that they can be captured, visualised and analysed directly from GIS software, along with data from other sources. The following figure illustrates how the PSA web map interface and services shall fit in a typical Planetary GIS user working environment.

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines.

PubMed

Barsnes, Harald; Vaudel, Marc

2018-05-25

Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in SearchGUI, a common open-source interface for the most frequently used freely available proteomics search and de novo engines that has evolved into a central component in numerous bioinformatics workflows.

WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

PubMed Central

Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

PubMed

Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

The CUAHSI Water Data Center: Empowering scientists to discover, use, store, and share water data

NASA Astrophysics Data System (ADS)

Couch, A. L.; Hooper, R. P.; Arrigo, J. S.

2012-12-01

The proposed CUAHSI Water Data Center (WDC) will provide production-quality water data resources based upon the successful large-scale data services prototype developed by the CUAHSI Hydrologic Information System (HIS) project. The WDC, using the HIS technology, concentrates on providing time series data collected at fixed points or on moving platforms from sensors primarily (but not exclusively) in the medium of water. The WDC's missions include providing simple and effective data discovery tools useful to researchers in a variety of water-related disciplines, and providing simple and cost-effective data publication mechanisms for projects that do not desire to run their own data servers. The WDC's activities will include: 1. Rigorous curation of the water data catalog already assembled during the CUAHSI HIS project, to ensure accuracy of records and existence of declared sources. 2. Data backup and failover services for "at risk" data sources. 3. Creation and support for ubiquitously accessible data discovery and access, web-based search and smartphone applications. 4. Partnerships with researchers to extend the state of the art in water data use. 5. Partnerships with industry to create plug-and-play data publishing from sensors, and to create domain-specific tools. The WDC will serve as a knowledge resource for researchers of water-related issues, and will interface with other data centers to make their data more accessible to water researchers. The WDC will serve as a vehicle for addressing some of the grand challenges of accessing and using water data, including: a. Cross-domain data discovery: different scientific domains refer to the same kind of water data using different terminologies, making discovery of data difficult for researchers outside the data provider's domain. b. Cross-validation of data sources: much water data comes from sources lacking rigorous quality control procedures; such sources can be compared against others with rigorous quality control. The WDC enables this by making both kinds of sources available in the same search interface. c. Data provenance: the appropriateness of data for use in a specific model or analysis often depends upon the exact details of how data was gathered and processed. The WDC will aid this by curating standards for metadata that are as descriptive as practical of the collection procedures. "Plug and play" sensor interfaces will fill in metadata appropriate to each sensor without human intervention. d. Contextual search: discovering data based upon geological (e.g. aquifer) or geographic (e.g., location in a stream network) features external to metadata. e. Data-driven search: discovering data that exhibit quality factors that are not described by the metadata. The WDC will partner with researchers desiring contextual and data driven search, and make results available to all. Many major data providers (e.g. federal agencies) are not mandated to provide access to data other than those they collect. The HIS project assembled data from over 90 different sources, thus demonstrating the promise of this approach. Meeting the grand challenges listed above will greatly enhance scientists' ability to discover, interpret, access, and analyze water data from across domains and sources to test Earth system hypotheses.

ADS Bumblebee comes of age

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto; Kurtz, Michael J.; Henneken, Edwin; Grant, Carolyn S.; Thompson, Donna M.; Chyla, Roman; McDonald, Steven; Shaulis, Taylor J.; Blanco-Cuaresma, Sergi; Shapurian, Golnaz; Hostetler, Timothy W.; Templeton, Matthew R.; Lockhart, Kelly E.

2018-01-01

The ADS Team has been working on a new system architecture and user interface named “ADS Bumblebee” since 2015. The new system presents many advantages over the traditional ADS interface and search engine (“ADS Classic”). A new, state of the art search engine features a number of new capabilities such as full-text search, advanced citation queries, filtering of results and scalable analytics for any search results. Its services are built on a cloud computing platform which can be easily scaled to match user demand. The Bumblebee user interface is a rich javascript application which leverages the features of the search engine and integrates a number of additional visualizations such as co-author and co-citation networks which provide a hierarchical view of research groups and research topics, respectively. Displays of paper analytics provide views of the basic article metrics (citations, reads, and age). All visualizations are interactive and provide ways to further refine search results. This new search system, which has been in beta for the past three years, has now matured to the point that it provides feature and content parity with ADS Classic, and has become the recommended way to access ADS content and services. Following a successful transition to Bumblebee, the use of ADS Classic will be discouraged starting in 2018 and phased out in 2019. You can access our new interface at https://ui.adsabs.harvard.edu

PcapDB: Search Optimized Packet Capture, Version 0.1.0.0

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

Ferrell, Paul; Steinfadt, Shannon

PcapDB is a packet capture system designed to optimize the captured data for fast search in the typical (network incident response) use case. The technology involved in this software has been submitted via the IDEAS system and has been filed as a provisional patent. It includes the following primary components: capture: The capture component utilizes existing capture libraries to retrieve packets from network interfaces. Once retrieved the packets are passed to additional threads for sorting into flows and indexing. The sorted flows and indexes are passed to other threads so that they can be written to disk. These components aremore » written in the C programming language. search: The search components provide a means to find relevant flows and the associated packets. A search query is parsed and represented as a search tree. Various search commands, written in C, are then used resolve this tree into a set of search results. The tree generation and search execution management components are written in python. interface: The PcapDB web interface is written in Python on the Django framework. It provides a series of pages, API's, and asynchronous tasks that allow the user to manage the capture system, perform searches, and retrieve results. Web page components are written in HTML,CSS and Javascript.« less

Flight Planning in the Cloud

NASA Technical Reports Server (NTRS)

Flores, Sarah L.; Chapman, Bruce D.; Tung, Waye W.; Zheng, Yang

2011-01-01

This new interface will enable Principal Investigators (PIs), as well as UAVSAR (Uninhabited Aerial Vehicle Synthetic Aperture Radar) members to do their own flight planning and time estimation without having to request flight lines through the science coordinator. It uses an all-in-one Google Maps interface, a JPL hosted database, and PI flight requirements to design an airborne flight plan. The application will enable users to see their own flight plan being constructed interactively through a map interface, and then the flight planning software will generate all the files necessary for the flight. Afterward, the UAVSAR team can then complete the flight request, including calendaring and supplying requisite flight request files in the expected format for processing by NASA s airborne science program. Some of the main features of the interface include drawing flight lines on the map, nudging them, adding them to the current flight plan, and reordering them. The user can also search and select takeoff, landing, and intermediate airports. As the flight plan is constructed, all of its components are constantly being saved to the database, and the estimated flight times are updated. Another feature is the ability to import flight lines from previously saved flight plans. One of the main motivations was to make this Web application as simple and intuitive as possible, while also being dynamic and robust. This Web application can easily be extended to support other airborne instruments.

Toward FRP-Based Brain-Machine Interfaces—Single-Trial Classification of Fixation-Related Potentials

PubMed Central

Finke, Andrea; Essig, Kai; Marchioro, Giuseppe; Ritter, Helge

2016-01-01

The co-registration of eye tracking and electroencephalography provides a holistic measure of ongoing cognitive processes. Recently, fixation-related potentials have been introduced to quantify the neural activity in such bi-modal recordings. Fixation-related potentials are time-locked to fixation onsets, just like event-related potentials are locked to stimulus onsets. Compared to existing electroencephalography-based brain-machine interfaces that depend on visual stimuli, fixation-related potentials have the advantages that they can be used in free, unconstrained viewing conditions and can also be classified on a single-trial level. Thus, fixation-related potentials have the potential to allow for conceptually different brain-machine interfaces that directly interpret cortical activity related to the visual processing of specific objects. However, existing research has investigated fixation-related potentials only with very restricted and highly unnatural stimuli in simple search tasks while participant’s body movements were restricted. We present a study where we relieved many of these restrictions while retaining some control by using a gaze-contingent visual search task. In our study, participants had to find a target object out of 12 complex and everyday objects presented on a screen while the electrical activity of the brain and eye movements were recorded simultaneously. Our results show that our proposed method for the classification of fixation-related potentials can clearly discriminate between fixations on relevant, non-relevant and background areas. Furthermore, we show that our classification approach generalizes not only to different test sets from the same participant, but also across participants. These results promise to open novel avenues for exploiting fixation-related potentials in electroencephalography-based brain-machine interfaces and thus providing a novel means for intuitive human-machine interaction. PMID:26812487

An Observation Knowledgebase for Hinode Data

NASA Astrophysics Data System (ADS)

Hurlburt, Neal E.; Freeland, S.; Green, S.; Schiff, D.; Seguin, R.; Slater, G.; Cirtain, J.

2007-05-01

We have developed a standards-based system for the Solar Optical and X Ray Telescopes on the Hinode orbiting solar observatory which can serve as part of a developing Heliophysics informatics system. Our goal is to make the scientific data acquired by Hinode more accessible and useful to scientists by allowing them to do reasoning and flexible searches on observation metadata and to ask higher-level questions of the system than previously allowed. The Hinode Observation Knowledgebase relates the intentions and goals of the observation planners (as-planned metadata) with actual observational data (as-run metadata), along with connections to related models, data products and identified features (follow-up metadata) through a citation system. Summaries of the data (both as image thumbnails and short "film strips") serve to guide researchers to the observations appropriate for their research, and these are linked directly to the data catalog for easy extraction and delivery. The semantic information of the observation (Field of view, wavelength, type of observable, average cadence etc.) is captured through simple user interfaces and encoded using the VOEvent XML standard (with the addition of some solar-related extensions). These interfaces merge metadata acquired automatically during both mission planning and an data analysis (see Seguin et. al. 2007 at this meeting) phases with that obtained directly from the planner/analyst and send them to be incorporated into the knowledgebase. The resulting information is automatically rendered into standard categories based on planned and recent observations, as well as by popularity and recommendations by the science team. They are also directly searchable through both and web-based searches and direct calls to the API. Observations details can also be rendered as RSS, iTunes and Google Earth interfaces. The resulting system provides a useful tool to researchers and can act as a demonstration for larger, more complex systems.

Unified User Interface to Support Effective and Intuitive Data Discovery, Dissemination, and Analysis at NASA GES DISC

NASA Technical Reports Server (NTRS)

Petrenko, M.; Hegde, M.; Bryant, K.; Johnson, J. E.; Ritrivi, A.; Shen, S.; Volmer, B.; Pham, L. B.

2015-01-01

Goddard Earth Sciences Data and Information Services Center (GES DISC) has been providing access to scientific data sets since 1990s. Beginning as one of the first Earth Observing System Data and Information System (EOSDIS) archive centers, GES DISC has evolved to offer a wide range of science-enabling services. With a growing understanding of needs and goals of its science users, GES DISC continues to improve and expand on its broad set of data discovery and access tools, sub-setting services, and visualization tools. Nonetheless, the multitude of the available tools, a partial overlap of functionality, and independent and uncoupled interfaces employed by these tools often leave the end users confused as of what tools or services are the most appropriate for a task at hand. As a result, some the services remain underutilized or largely unknown to the users, significantly reducing the availability of the data and leading to a great loss of scientific productivity. In order to improve the accessibility of GES DISC tools and services, we have designed and implemented UUI, the Unified User Interface. UUI seeks to provide a simple, unified, and intuitive one-stop shop experience for the key services available at GES DISC, including sub-setting (Simple Subset Wizard), granule file search (Mirador), plotting (Giovanni), and other services. In this poster, we will discuss the main lessons, obstacles, and insights encountered while designing the UUI experience. We will also present the architecture and technology behind UUI, including NodeJS, Angular, and Mongo DB, as well as speculate on the future of the tool at GES DISC as well as in a broader context of the Space Science Informatics.

Gener: a minimal programming module for chemical controllers based on DNA strand displacement

PubMed Central

Kahramanoğulları, Ozan; Cardelli, Luca

2015-01-01

Summary: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX. Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. Contact: ozan@cosbi.eu PMID:25957353

Gener: a minimal programming module for chemical controllers based on DNA strand displacement.

PubMed

Kahramanoğulları, Ozan; Cardelli, Luca

2015-09-01

: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research's DSD tool as well as to LaTeX. Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. ozan@cosbi.eu. © The Author 2015. Published by Oxford University Press.

Transfer Learning to Accelerate Interface Structure Searches

NASA Astrophysics Data System (ADS)

Oda, Hiromi; Kiyohara, Shin; Tsuda, Koji; Mizoguchi, Teruyasu

2017-12-01

Interfaces have atomic structures that are significantly different from those in the bulk, and play crucial roles in material properties. The central structures at the interfaces that provide properties have been extensively investigated. However, determination of even one interface structure requires searching for the stable configuration among many thousands of candidates. Here, a powerful combination of machine learning techniques based on kriging and transfer learning (TL) is proposed as a method for unveiling the interface structures. Using the kriging+TL method, thirty-three grain boundaries were systematically determined from 1,650,660 candidates in only 462 calculations, representing an increase in efficiency over conventional all-candidate calculation methods, by a factor of approximately 3,600.

Developing A Web-based User Interface for Semantic Information Retrieval

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2003-01-01

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc

Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

Development of user-centered interfaces to search the knowledge resources of the Virginia Henderson International Nursing Library.

PubMed

Jones, Josette; Harris, Marcelline; Bagley-Thompson, Cheryl; Root, Jane

2003-01-01

This poster describes the development of user-centered interfaces in order to extend the functionality of the Virginia Henderson International Nursing Library (VHINL) from library to web based portal to nursing knowledge resources. The existing knowledge structure and computational models are revised and made complementary. Nurses' search behavior is captured and analyzed, and the resulting search models are mapped to the revised knowledge structure and computational model.

Designing Search: Effective Search Interfaces for Academic Library Web Sites

ERIC Educational Resources Information Center

Teague-Rector, Susan; Ghaphery, Jimmy

2008-01-01

Academic libraries customize, support, and provide access to myriad information systems, each with complex graphical user interfaces. The number of possible information entry points on an academic library Web site is both daunting to the end-user and consistently challenging to library Web site designers. Faced with the challenges inherent in…

An ADC Interface for the Apple II.

ERIC Educational Resources Information Center

Leiker, P. Steven

1990-01-01

Described is the construction of a simple analog-to-digital convertor circuit to interface an Apple II+ microcomputer to a light sensor used in conjunction with a holographic gear inspector. A list of parts, circuit diagram, and a simple BASIC program for the convertor are provided. (CW)

XSemantic: An Extension of LCA Based XML Semantic Search

NASA Astrophysics Data System (ADS)

Supasitthimethee, Umaporn; Shimizu, Toshiyuki; Yoshikawa, Masatoshi; Porkaew, Kriengkrai

One of the most convenient ways to query XML data is a keyword search because it does not require any knowledge of XML structure or learning a new user interface. However, the keyword search is ambiguous. The users may use different terms to search for the same information. Furthermore, it is difficult for a system to decide which node is likely to be chosen as a return node and how much information should be included in the result. To address these challenges, we propose an XML semantic search based on keywords called XSemantic. On the one hand, we give three definitions to complete in terms of semantics. Firstly, the semantic term expansion, our system is robust from the ambiguous keywords by using the domain ontology. Secondly, to return semantic meaningful answers, we automatically infer the return information from the user queries and take advantage of the shortest path to return meaningful connections between keywords. Thirdly, we present the semantic ranking that reflects the degree of similarity as well as the semantic relationship so that the search results with the higher relevance are presented to the users first. On the other hand, in the LCA and the proximity search approaches, we investigated the problem of information included in the search results. Therefore, we introduce the notion of the Lowest Common Element Ancestor (LCEA) and define our simple rule without any requirement on the schema information such as the DTD or XML Schema. The first experiment indicated that XSemantic not only properly infers the return information but also generates compact meaningful results. Additionally, the benefits of our proposed semantics are demonstrated by the second experiment.

The IRIS Federator: Accessing Seismological Data Across Data Centers

NASA Astrophysics Data System (ADS)

Trabant, C. M.; Van Fossen, M.; Ahern, T. K.; Weekly, R. T.

2015-12-01

In 2013 the International Federation of Digital Seismograph Networks (FDSN) approved a specification for web service interfaces for accessing seismological station metadata, time series and event parameters. Since then, a number of seismological data centers have implemented FDSN service interfaces, with more implementations in development. We have developed a new system called the IRIS Federator which leverages this standardization and provides the scientific community with a service for easy discovery and access of seismological data across FDSN data centers. These centers are located throughout the world and this work represents one model of a system for data collection across geographic and political boundaries.The main components of the IRIS Federator are a catalog of time series metadata holdings at each data center and a web service interface for searching the catalog. The service interface is designed to support client­-side federated data access, a model in which the client (software run by the user) queries the catalog and then collects the data from each identified center. By default the results are returned in a format suitable for direct submission to those web services, but could also be formatted in a simple text format for general data discovery purposes. The interface will remove any duplication of time series channels between data centers according to a set of business rules by default, however a user may request results with all duplicate time series entries included. We will demonstrate how client­-side federation is being incorporated into some of the DMC's data access tools. We anticipate further enhancement of the IRIS Federator to improve data discovery in various scenarios and to improve usefulness to communities beyond seismology.Data centers with FDSN web services: http://www.fdsn.org/webservices/The IRIS Federator query interface: http://service.iris.edu/irisws/fedcatalog/1/

GENESI-DR Portal: a scientific gateway to distributed repositories

NASA Astrophysics Data System (ADS)

Goncalves, Pedro; Brito, Fabrice; D'Andria, Fabio; Cossu, Roberto; Fusco, Luigi

2010-05-01

GENESI-DR (Ground European Network for Earth Science Interoperations - Digital Repositories) is a European Commission (EC)-funded project, kicked-off early 2008 lead by ESA; partners include Space Agencies (DLR, ASI, CNES), both space and no-space data providers such as ENEA (I), Infoterra (UK), K-SAT (N), NILU (N), JRC (EU) and industry as Elsag Datamat (I), CS (F) and TERRADUE (I). GENESI-DR intends to meet the challenge of facilitating "time to science" from different Earth Science disciplines in discovery, access and use (combining, integrating, processing, …) of historical and recent Earth-related data from space, airborne and in-situ sensors, which are archived in large distributed repositories. "Discovering" which data are available on a "geospatial web" is one of the main challenges ES scientists have to face today. Some well- known data sets are referred to in many places, available from many sources. For core information with a common purpose many copies are distributed, e.g., VMap0, Landsat, and SRTM. Other data sets in low or local demand may only be found in a few places and niche communities. Relevant services, results of analysis, applications and tools are accessible in a very scattered and uncoordinated way, often through individual initiatives from Earth Observation mission operators, scientific institutes dealing with ground measurements, service companies or data catalogues. In the discourse of Spatial Data Infrastructures, there are "catalogue services" - directories containing information on where spatial data and services can be found. For metadata "records" describing spatial data and services, there are "registries". The Geospatial industry coins specifications for search interfaces, where it might do better to reach out to other information retrieval and Internet communities. These considerations are the basis for the GENESI-DR scientific portal, which adopts a simple model allowing the geo-spatial classification and discovery of information as a loosely connected federation of nodes. This network had however to be resilient to node failures and able to scale with the growing addition of new information about data and services. The GENESI-DR scientific portal is still evolving as the project deploys the different components amongst the different partners, but the aim is to provide the connection to information, establish rights, access it and in some cases apply algorithms using the computer power available on the infrastructure with simple interfaces. As information is discovered in the network, it can be further exploited, filtered or enhanced according to the user goals. To implement this vision two specialized graphical interfaces were designed on the portal. The first, concentrates on the text-based search of information, while the second is a command and control of submission and order status on a distributed processing environment. The text search uses natural language features that extract the spatial temporal components from the user query. This is then propagated to the nodes by mapping them to OpenSearch extensions, and then returned to the user as an aggregated list of the resources. These can either be access points to dataset series or services that can be further analysed and processed. At this stage, the user is presented with dedicated interfaces that correspond to context of the action that is performing. Be it a bulk data download, data processing or data mining, the different services offer specialized interfaces that are integrated on the portal. In the overall, the GENESI-DR project identifies best practices and supporting context for the use of a minimal abstract model to loosely connect a federation of Digital Repositories. Surpassing the apparent lack of cost effectiveness of the Spatial Data Infrastructures effort in developing "catalogue services" is achieved by trimming the use cases to the most common and relevant. The GENESI-DR scientific portal is, as such, the visible front-end of a dedicated infrastructure providing transparent access to information and allowing Earth Science communities to easily and quickly derive objective information and share knowledge based on all environmentally sensitive domains.

Lyceum: A Multi-Protocol Digital Library Gateway

NASA Technical Reports Server (NTRS)

Maa, Ming-Hokng; Nelson, Michael L.; Esler, Sandra L.

1997-01-01

Lyceum is a prototype scalable query gateway that provides a logically central interface to multi-protocol and physically distributed, digital libraries of scientific and technical information. Lyceum processes queries to multiple syntactically distinct search engines used by various distributed information servers from a single logically central interface without modification of the remote search engines. A working prototype (http://www.larc.nasa.gov/lyceum/) demonstrates the capabilities, potentials, and advantages of this type of meta-search engine by providing access to over 50 servers covering over 20 disciplines.

PhenoTips: patient phenotyping software for clinical and research use.

PubMed

Girdea, Marta; Dumitriu, Sergiu; Fiume, Marc; Bowdin, Sarah; Boycott, Kym M; Chénier, Sébastien; Chitayat, David; Faghfoury, Hanna; Meyn, M Stephen; Ray, Peter N; So, Joyce; Stavropoulos, Dimitri J; Brudno, Michael

2013-08-01

We have developed PhenoTips: open source software for collecting and analyzing phenotypic information for patients with genetic disorders. Our software combines an easy-to-use interface, compatible with any device that runs a Web browser, with a standardized database back end. The PhenoTips' user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and additional notes. Phenotypic information is represented using the Human Phenotype Ontology; however, the complexity of the ontology is hidden behind a user interface, which combines simple selection of common phenotypes with error-tolerant, predictive search of the entire ontology. PhenoTips supports accurate diagnosis by analyzing the entered data, then suggesting additional clinical investigations and providing Online Mendelian Inheritance in Man (OMIM) links to likely disorders. By collecting, classifying, and analyzing phenotypic information during the patient encounter, PhenoTips allows for streamlining of clinic workflow, efficient data entry, improved diagnosis, standardization of collected patient phenotypes, and sharing of anonymized patient phenotype data for the study of rare disorders. Our source code and a demo version of PhenoTips are available at http://phenotips.org. © 2013 WILEY PERIODICALS, INC.

How to improve your PubMed/MEDLINE searches: 3. advanced searching, MeSH and My NCBI.

PubMed

Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

2014-03-01

Although the basic PubMed search is often helpful, the results may sometimes be non-specific. For more control over the search process you can use the Advanced Search Builder interface. This allows a targeted search in specific fields, with the convenience of being able to select the intended search field from a list. It also provides a history of your previous searches. The search history is useful to develop a complex search query by combining several previous searches using Boolean operators. For indexing the articles in MEDLINE, the NLM uses a controlled vocabulary system called MeSH. This standardised vocabulary solves the problem of authors, researchers and librarians who may use different terms for the same concept. To be efficient in a PubMed search, you should start by identifying the most appropriate MeSH terms and use them in your search where possible. My NCBI is a personal workspace facility available through PubMed and makes it possible to customise the PubMed interface. It provides various capabilities that can enhance your search performance.

Using the Proteomics Identifications Database (PRIDE).

PubMed

Martens, Lennart; Jones, Phil; Côté, Richard

2008-03-01

The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer-reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE.

Searching the SOHO online catalogs

NASA Technical Reports Server (NTRS)

Thompson, William; Yurow, Ron

1994-01-01

The SOHO on-line catalogs will contain information about the observations from several made or planned campaigns, that must be available to scientists who wish to use SOHO data. The World Wide Web (WWW) was chosen as the interface to the SOHO on-line catalogs, because it is easy to use, well suited to a geographically distributed user community, and freely available. Through the use of a forms-capable WWW client such as Mosaic or Lynx, a scientist will be able to browse through the catalogs of observations in a very simple, self explanatory way. Data files can then be selected from the returned lists for either immediate transferring or sending on tape by mail, with appropriate checks for whether data is in the public domain or not.

Perspectives on theory at the interface of physics and biology.

PubMed

Bialek, William

2018-01-01

Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. I am an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples.

Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.

PubMed

Eppig, Janan T; Smith, Cynthia L; Blake, Judith A; Ringwald, Martin; Kadin, James A; Richardson, Joel E; Bult, Carol J

2017-01-01

The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.

Perspectives on theory at the interface of physics and biology

NASA Astrophysics Data System (ADS)

Bialek, William

2018-01-01

Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. I am an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples.

Search systems and computer-implemented search methods

DOEpatents

Payne, Deborah A.; Burtner, Edwin R.; Hampton, Shawn D.; Gillen, David S.; Henry, Michael J.

2017-03-07

Search systems and computer-implemented search methods are described. In one aspect, a search system includes a communications interface configured to access a plurality of data items of a collection, wherein the data items include a plurality of image objects individually comprising image data utilized to generate an image of the respective data item. The search system may include processing circuitry coupled with the communications interface and configured to process the image data of the data items of the collection to identify a plurality of image content facets which are indicative of image content contained within the images and to associate the image objects with the image content facets and a display coupled with the processing circuitry and configured to depict the image objects associated with the image content facets.

Search systems and computer-implemented search methods

DOEpatents

Payne, Deborah A.; Burtner, Edwin R.; Bohn, Shawn J.; Hampton, Shawn D.; Gillen, David S.; Henry, Michael J.

2015-12-22

Search systems and computer-implemented search methods are described. In one aspect, a search system includes a communications interface configured to access a plurality of data items of a collection, wherein the data items include a plurality of image objects individually comprising image data utilized to generate an image of the respective data item. The search system may include processing circuitry coupled with the communications interface and configured to process the image data of the data items of the collection to identify a plurality of image content facets which are indicative of image content contained within the images and to associate the image objects with the image content facets and a display coupled with the processing circuitry and configured to depict the image objects associated with the image content facets.

Interaction of a sodium ion with the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1989-01-01

Molecular dynamics results are presented for the density profile of a sodium ion near the water liquid-vapor interface at 320 K. These results are compared with the predictions of a simple dielectric model for the interaction of a monovalent ion with this interface. The interfacial region described by the model profile is too narrow and the profile decreases too abruptly near the solution interface. Thus, the simple model does not provide a satisfactory description of the molecular dynamics results for ion positions within two molecular diameters from the solution interface where appreciable ion concentrations are observed. These results suggest that surfaces associated with dielectric models of ionic processes at aqueous solution interfaces should be located at least two molecular diameters inside the liquid phase. A free energy expense of about 2 kcal/mol is required to move the ion within two molecular layers of the free water liquid-vapor interface.

Magnetocapacitance and the physics of solid state interfaces

NASA Astrophysics Data System (ADS)

Hebard, Arthur

2008-10-01

When Herbert Kroemer stated in his Nobel address [1] that ``the interface is the device,'' he was implicitly acknowledging the importance of understanding the physics of interfaces. If interfaces are to have character traits, then ``impedance'' (or complex capacitance) would be a commonly used descriptor. In this talk I will discuss the use of magnetic fields to probe the ``character'' of a variety of interfaces including planar capacitor structures with magnetic electrodes, simple metal/semiconductor contacts (Schottky barriers) and the interface-dominated competition on microscopic length scales between ferromagnetic metallic and charge-ordered insulating phases in complex oxides. I will show that seeking experimental answers to surprisingly simple questions often leads to striking results that seriously challenge theoretical understanding. Perhaps Herbert Kroemer should have said, ``the interface is the device with a magnetic personality that continually surprises.'' [3pt] [1] Herbert Kroemer, ``Quasielectric fields and band offsets: teaching electron s new tricks,'' Nobel Lecture, December 8, 2000:

p3d--Python module for structural bioinformatics.

PubMed

Fufezan, Christian; Specht, Michael

2009-08-21

High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

PubMed

Li, Pei; Ji, Guoli; Dong, Min; Schmidt, Emily; Lenox, Douglas; Chen, Liangliang; Liu, Qi; Liu, Lin; Zhang, Jie; Liang, Chun

2012-09-15

To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn Supplementary data are available at Bioinformatics online.

Operational Support for Instrument Stability through ODI-PPA Metadata Visualization and Analysis

NASA Astrophysics Data System (ADS)

Young, M. D.; Hayashi, S.; Gopu, A.; Kotulla, R.; Harbeck, D.; Liu, W.

2015-09-01

Over long time scales, quality assurance metrics taken from calibration and calibrated data products can aid observatory operations in quantifying the performance and stability of the instrument, and identify potential areas of concern or guide troubleshooting and engineering efforts. Such methods traditionally require manual SQL entries, assuming the requisite metadata has even been ingested into a database. With the ODI-PPA system, QA metadata has been harvested and indexed for all data products produced over the life of the instrument. In this paper we will describe how, utilizing the industry standard Highcharts Javascript charting package with a customized AngularJS-driven user interface, we have made the process of visualizing the long-term behavior of these QA metadata simple and easily replicated. Operators can easily craft a custom query using the powerful and flexible ODI-PPA search interface and visualize the associated metadata in a variety of ways. These customized visualizations can be bookmarked, shared, or embedded externally, and will be dynamically updated as new data products enter the system, enabling operators to monitor the long-term health of their instrument with ease.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

PubMed

Uszkoreit, Julian; Maerkens, Alexandra; Perez-Riverol, Yasset; Meyer, Helmut E; Marcus, Katrin; Stephan, Christian; Kohlbacher, Oliver; Eisenacher, Martin

2015-07-02

Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.

Interface Psychology: Touchscreens Change Attribute Importance, Decision Criteria, and Behavior in Online Choice

PubMed Central

Gips, James

2015-01-01

Abstract As the rise of tablets and smartphones move the dominant interface for digital content from mouse or trackpad to direct touchscreen interaction, work is needed to explore the role of interfaces in shaping psychological reactions to online content. This research explores the role of direct-touch interfaces in product search and choice, and isolates the touch element from other form factor changes such as screen size. Results from an experimental study using a travel recommendation Web site show that a direct-touch interface (vs. a more traditional mouse interface) increases the number of alternatives searched, and biases evaluations toward tangible attributes such as décor and furniture over intangible attributes such as WiFi and employee demeanor. Direct-touch interfaces also elevate the importance of internal and subjective satisfaction metrics such as instinct over external and objective metrics such as reviews, which in turn increases anticipated satisfaction metrics. Findings suggest that interfaces can strongly affect how online content is explored, perceived, remembered, and acted on, and further work in interface psychology could be as fruitful as research exploring the content itself. PMID:26348814

Interface Psychology: Touchscreens Change Attribute Importance, Decision Criteria, and Behavior in Online Choice.

PubMed

Brasel, S Adam; Gips, James

2015-09-01

As the rise of tablets and smartphones move the dominant interface for digital content from mouse or trackpad to direct touchscreen interaction, work is needed to explore the role of interfaces in shaping psychological reactions to online content. This research explores the role of direct-touch interfaces in product search and choice, and isolates the touch element from other form factor changes such as screen size. Results from an experimental study using a travel recommendation Web site show that a direct-touch interface (vs. a more traditional mouse interface) increases the number of alternatives searched, and biases evaluations toward tangible attributes such as décor and furniture over intangible attributes such as WiFi and employee demeanor. Direct-touch interfaces also elevate the importance of internal and subjective satisfaction metrics such as instinct over external and objective metrics such as reviews, which in turn increases anticipated satisfaction metrics. Findings suggest that interfaces can strongly affect how online content is explored, perceived, remembered, and acted on, and further work in interface psychology could be as fruitful as research exploring the content itself.

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.

Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE.

PubMed

Demelo, Jonathan; Parsons, Paul; Sedig, Kamran

2017-02-02

Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks. Our objective was to improve support for exploratory search tasks by combining two strategies in the design of an interactive visual interface by (1) using a formal ontology to help users build domain-specific knowledge and vocabulary and (2) providing multi-stage triaging support to help mitigate the information overload problem. We developed a Web-based tool, Ontology-Driven Visual Search and Triage Interface for MEDLINE (OVERT-MED), to test our design ideas. We implemented a custom searchable index of MEDLINE, which comprises approximately 25 million document citations. We chose a popular biomedical ontology, the Human Phenotype Ontology (HPO), to test our solution to the vocabulary problem. We implemented multistage triaging support in OVERT-MED, with the aid of interactive visualization techniques, to help users deal with large document sets returned from searches. Formative evaluation suggests that the design features in OVERT-MED are helpful in addressing the two major difficulties described above. Using a formal ontology seems to help users articulate their information needs with more accurate vocabulary. In addition, multistage triaging combined with interactive visualizations shows promise in mitigating the information overload problem. Our strategies appear to be valuable in addressing the two major problems in exploratory search. Although we tested OVERT-MED with a particular ontology and document collection, we anticipate that our strategies can be transferred successfully to other contexts. ©Jonathan Demelo, Paul Parsons, Kamran Sedig. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 02.02.2017.

Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE

PubMed Central

2017-01-01

Background Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks. Objective Our objective was to improve support for exploratory search tasks by combining two strategies in the design of an interactive visual interface by (1) using a formal ontology to help users build domain-specific knowledge and vocabulary and (2) providing multi-stage triaging support to help mitigate the information overload problem. Methods We developed a Web-based tool, Ontology-Driven Visual Search and Triage Interface for MEDLINE (OVERT-MED), to test our design ideas. We implemented a custom searchable index of MEDLINE, which comprises approximately 25 million document citations. We chose a popular biomedical ontology, the Human Phenotype Ontology (HPO), to test our solution to the vocabulary problem. We implemented multistage triaging support in OVERT-MED, with the aid of interactive visualization techniques, to help users deal with large document sets returned from searches. Results Formative evaluation suggests that the design features in OVERT-MED are helpful in addressing the two major difficulties described above. Using a formal ontology seems to help users articulate their information needs with more accurate vocabulary. In addition, multistage triaging combined with interactive visualizations shows promise in mitigating the information overload problem. Conclusions Our strategies appear to be valuable in addressing the two major problems in exploratory search. Although we tested OVERT-MED with a particular ontology and document collection, we anticipate that our strategies can be transferred successfully to other contexts. PMID:28153818

A Shared Infrastructure for Federated Search Across Distributed Scientific Metadata Catalogs

NASA Astrophysics Data System (ADS)

Reed, S. A.; Truslove, I.; Billingsley, B. W.; Grauch, A.; Harper, D.; Kovarik, J.; Lopez, L.; Liu, M.; Brandt, M.

2013-12-01

The vast amount of science metadata can be overwhelming and highly complex. Comprehensive analysis and sharing of metadata is difficult since institutions often publish to their own repositories. There are many disjoint standards used for publishing scientific data, making it difficult to discover and share information from different sources. Services that publish metadata catalogs often have different protocols, formats, and semantics. The research community is limited by the exclusivity of separate metadata catalogs and thus it is desirable to have federated search interfaces capable of unified search queries across multiple sources. Aggregation of metadata catalogs also enables users to critique metadata more rigorously. With these motivations in mind, the National Snow and Ice Data Center (NSIDC) and Advanced Cooperative Arctic Data and Information Service (ACADIS) implemented two search interfaces for the community. Both the NSIDC Search and ACADIS Arctic Data Explorer (ADE) use a common infrastructure which keeps maintenance costs low. The search clients are designed to make OpenSearch requests against Solr, an Open Source search platform. Solr applies indexes to specific fields of the metadata which in this instance optimizes queries containing keywords, spatial bounds and temporal ranges. NSIDC metadata is reused by both search interfaces but the ADE also brokers additional sources. Users can quickly find relevant metadata with minimal effort and ultimately lowers costs for research. This presentation will highlight the reuse of data and code between NSIDC and ACADIS, discuss challenges and milestones for each project, and will identify creation and use of Open Source libraries.

Combining local and global limitations of visual search.

PubMed

Põder, Endel

2017-04-01

There are different opinions about the roles of local interactions and central processing capacity in visual search. This study attempts to clarify the problem using a new version of relevant set cueing. A central precue indicates two symmetrical segments (that may contain a target object) within a circular array of objects presented briefly around the fixation point. The number of objects in the relevant segments, and density of objects in the array were varied independently. Three types of search experiments were run: (a) search for a simple visual feature (color, size, and orientation); (b) conjunctions of simple features; and (c) spatial configuration of simple features (rotated Ts). For spatial configuration stimuli, the results were consistent with a fixed global processing capacity and standard crowding zones. For simple features and their conjunctions, the results were different, dependent on the features involved. While color search exhibits virtually no capacity limits or crowding, search for an orientation target was limited by both. Results for conjunctions of features can be partly explained by the results from the respective features. This study shows that visual search is limited by both local interference and global capacity, and the limitations are different for different visual features.

[Study on Information Extraction of Clinic Expert Information from Hospital Portals].

PubMed

Zhang, Yuanpeng; Dong, Jiancheng; Qian, Danmin; Geng, Xingyun; Wu, Huiqun; Wang, Li

2015-12-01

Clinic expert information provides important references for residents in need of hospital care. Usually, such information is hidden in the deep web and cannot be directly indexed by search engines. To extract clinic expert information from the deep web, the first challenge is to make a judgment on forms. This paper proposes a novel method based on a domain model, which is a tree structure constructed by the attributes of search interfaces. With this model, search interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from the returned web pages indexed by search interfaces. To filter the noise information on a web page, a block importance model is proposed. The experiment results indicated that the domain model yielded a precision 10.83% higher than that of the rule-based method, whereas the block importance model yielded an F₁ measure 10.5% higher than that of the XPath method.

PubMedReco: A Real-Time Recommender System for PubMed Citations.

PubMed

Samuel, Hamman W; Zaïane, Osmar R

2017-01-01

We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous communication environment such as a chat room. Normally, users would have to leave their chat interface to open a new web browser window, and formulate an appropriate search query to retrieve relevant results. PubMedReco automatically generates the search query and shows relevant citations within the same integrated user interface. PubMedReco analyzes relevant keywords associated with the conversation and uses them to search for relevant citations using the PubMed E-utilities programming interface. Our contributions include improvements to the user experience for searching PubMed from within health forums and chat rooms, and a machine learning model for identifying relevant keywords. We demonstrate the feasibility of PubMedReco using BMJ's Doc2Doc forum discussions.

Peeling the Onion: Okapi System Architecture and Software Design Issues.

ERIC Educational Resources Information Center

Jones, S.; And Others

1997-01-01

Discusses software design issues for Okapi, an information retrieval system that incorporates both search engine and user interface and supports weighted searching, relevance feedback, and query expansion. The basic search system, adjacency searching, and moving toward a distributed system are discussed. (Author/LRW)

Omicseq: a web-based search engine for exploring omics datasets

PubMed Central

Sun, Xiaobo; Pittard, William S.; Xu, Tianlei; Chen, Li; Zwick, Michael E.; Jiang, Xiaoqian; Wang, Fusheng

2017-01-01

Abstract The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. PMID:28402462

A Detailed Analysis of End-User Search Behaviors.

ERIC Educational Resources Information Center

Wildemuth, Barbara M.; And Others

1991-01-01

Discussion of search strategy formulation focuses on a study at the University of North Carolina at Chapel Hill that analyzed how medical students developed and revised search strategies for microbiology database searches. Implications for future research on search behavior, for system interface design, and for end user training are suggested. (16…

BioModels Database: a repository of mathematical models of biological processes.

PubMed

Chelliah, Vijayalakshmi; Laibe, Camille; Le Novère, Nicolas

2013-01-01

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

PlantTFDB: a comprehensive plant transcription factor database

PubMed Central

Guo, An-Yuan; Chen, Xin; Gao, Ge; Zhang, He; Zhu, Qi-Hui; Liu, Xiao-Chuan; Zhong, Ying-Fu; Gu, Xiaocheng; He, Kun; Luo, Jingchu

2008-01-01

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26 402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis. PMID:17933783

Study on user interface of pathology picture archiving and communication system.

PubMed

Kim, Dasueran; Kang, Peter; Yun, Jungmin; Park, Sung-Hye; Seo, Jeong-Wook; Park, Peom

2014-01-01

It is necessary to improve the pathology workflow. A workflow task analysis was performed using a pathology picture archiving and communication system (pathology PACS) in order to propose a user interface for the Pathology PACS considering user experience. An interface analysis of the Pathology PACS in Seoul National University Hospital and a task analysis of the pathology workflow were performed by observing recorded video. Based on obtained results, a user interface for the Pathology PACS was proposed. Hierarchical task analysis of Pathology PACS was classified into 17 tasks including 1) pre-operation, 2) text, 3) images, 4) medical record viewer, 5) screen transition, 6) pathology identification number input, 7) admission date input, 8) diagnosis doctor, 9) diagnosis code, 10) diagnosis, 11) pathology identification number check box, 12) presence or absence of images, 13) search, 14) clear, 15) Excel save, 16) search results, and 17) re-search. And frequently used menu items were identified and schematized. A user interface for the Pathology PACS considering user experience could be proposed as a preliminary step, and this study may contribute to the development of medical information systems based on user experience and usability.

Graphical User Interface Programming in Introductory Computer Science.

ERIC Educational Resources Information Center

Skolnick, Michael M.; Spooner, David L.

Modern computing systems exploit graphical user interfaces for interaction with users; as a result, introductory computer science courses must begin to teach the principles underlying such interfaces. This paper presents an approach to graphical user interface (GUI) implementation that is simple enough for beginning students to understand, yet…

Quantifying medical student clinical experiences via an ICD Code Logging App.

PubMed

Rawlins, Fred; Sumpter, Cameron; Sutphin, Dean; Garner, Harold R

2018-03-01

The logging of ICD Diagnostic, Procedure and Drug codes is one means of tracking the experience of medical students' clinical rotations. The goal is to create a web-based computer and mobile application to track the progress of trainees, monitor the effectiveness of their training locations and be a means of sampling public health status. We have developed a web-based app in which medical trainees make entries via a simple and quick interface optimized for both mobile devices and personal computers. For each patient interaction, users enter ICD diagnostic, procedure, and drug codes via a hierarchical or search entry interface, as well as patient demographics (age range and gender, but no personal identifiers), and free-text notes. Users and administrators can review and edit input via a series of output interfaces. The user interface and back-end database are provided via dual redundant failover Linux servers. Students master the interface in ten minutes, and thereafter complete entries in less than one minute. Five hundred-forty 3rd year VCOM students each averaged 100 entries in the first four week clinical rotation. Data accumulated in various Appalachian clinics and Central American medical mission trips has demonstrated the public health surveillance utility of the application. PC and mobile apps can be used to collect medical trainee experience in real time or near real-time, quickly, and efficiently. This system has collected 75,596 entries to date, less than 2% of trainees have needed assistance to become proficient, and medical school administrators are using the various summaries to evaluate students and compare different rotation sites. Copyright © 2017. Published by Elsevier B.V.

A universal preconditioner for simulating condensed phase materials.

PubMed

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

A universal preconditioner for simulating condensed phase materials

NASA Astrophysics Data System (ADS)

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-01

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

ExplorEnz: the primary source of the IUBMB enzyme list

PubMed Central

McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

2009-01-01

ExplorEnz is the MySQL database that is used for the curation and dissemination of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature. A simple web-based query interface is provided, along with an advanced search engine for more complex Boolean queries. The WWW front-end is accessible at http://www.enzyme-database.org, from where downloads of the database as SQL and XML are also available. An associated form-based curatorial application has been developed to facilitate the curation of enzyme data as well as the internal and public review processes that occur before an enzyme entry is made official. Suggestions for new enzyme entries, or modifications to existing ones, can be made using the forms provided at http://www.enzyme-database.org/forms.php. PMID:18776214

Human-Robot Interface: Issues in Operator Performance, Interface Design, and Technologies

DTIC Science & Technology

2006-07-01

and the use of lightweight portable robotic sensor platforms. 5 robotics has reached a point where some generalities of HRI transcend specific...displays with control devices such as joysticks, wheels, and pedals (Kamsickas, 2003). Typical control stations include panels displaying (a) sensor ...tasks that do not involve mobility and usually involve camera control or data fusion from sensors Active search: Search tasks that involve mobility

Full Text and Figure Display Improves Bioscience Literature Search

PubMed Central

Divoli, Anna; Wooldridge, Michael A.; Hearst, Marti A.

2010-01-01

When reading bioscience journal articles, many researchers focus attention on the figures and their captions. This observation led to the development of the BioText literature search engine [1], a freely available Web-based application that allows biologists to search over the contents of Open Access Journals, and see figures from the articles displayed directly in the search results. This article presents a qualitative assessment of this system in the form of a usability study with 20 biologist participants using and commenting on the system. 19 out of 20 participants expressed a desire to use a bioscience literature search engine that displays articles' figures alongside the full text search results. 15 out of 20 participants said they would use a caption search and figure display interface either frequently or sometimes, while 4 said rarely and 1 said undecided. 10 out of 20 participants said they would use a tool for searching the text of tables and their captions either frequently or sometimes, while 7 said they would use it rarely if at all, 2 said they would never use it, and 1 was undecided. This study found evidence, supporting results of an earlier study, that bioscience literature search systems such as PubMed should show figures from articles alongside search results. It also found evidence that full text and captions should be searched along with the article title, metadata, and abstract. Finally, for a subset of users and information needs, allowing for explicit search within captions for figures and tables is a useful function, but it is not entirely clear how to cleanly integrate this within a more general literature search interface. Such a facility supports Open Access publishing efforts, as it requires access to full text of documents and the lifting of restrictions in order to show figures in the search interface. PMID:20418942

Searching Databases without Query-Building Aids: Implications for Dyslexic Users

ERIC Educational Resources Information Center

Berget, Gerd; Sandnes, Frode Eika

2015-01-01

Introduction: Few studies document the information searching behaviour of users with cognitive impairments. This paper therefore addresses the effect of dyslexia on information searching in a database with no tolerance for spelling errors and no query-building aids. The purpose was to identify effective search interface design guidelines that…

Geologic Materials Center - Inventory | Alaska Division of Geological &

Science.gov Websites

Alaska Visiting Alaska State Employees DGGS State of Alaska search Department of Natural Resources Reports Employment Staff Directory Publications Search Statewide Maps New Releases Sales Interactive Maps - Inventory Inventory Search Find GMC Inventory Samples The search interface functionality is dependent on the

(Meta)Search like Google

ERIC Educational Resources Information Center

Rochkind, Jonathan

2007-01-01

The ability to search and receive results in more than one database through a single interface--or metasearch--is something many users want. Google Scholar--the search engine of specifically scholarly content--and library metasearch products like Ex Libris's MetaLib, Serials Solution's Central Search, WebFeat, and products based on MuseGlobal used…

J-Plus Web Portal

NASA Astrophysics Data System (ADS)

Civera Lorenzo, Tamara

2017-10-01

Brief presentation about the J-PLUS EDR data access web portal (http://archive.cefca.es/catalogues/jplus-edr) where the different services available to retrieve images and catalogues data have been presented.J-PLUS Early Data Release (EDR) archive includes two types of data: images and dual and single catalogue data which include parameters measured from images. J-PLUS web portal offers catalogue data and images through several different online data access tools or services each suited to a particular need. The different services offered are: Coverage map Sky navigator Object visualization Image search Cone search Object list search Virtual observatory services: Simple Cone Search Simple Image Access Protocol Simple Spectral Access Protocol Table Access Protocol

Tendon Healing in Bone Tunnel after Human Anterior Cruciate Ligament Reconstruction: A Systematic Review of Histological Results.

PubMed

Lu, Hongbin; Chen, Can; Xie, Shanshan; Tang, Yifu; Qu, Jin

2018-05-21

Most studies concerning to tendon healing and incorporation into bone are mainly based on animal studies due to the invasive nature of the biopsy procedure. The evidence considering tendon graft healing to bone in humans is limited in several case series or case reports, and therefore, it is difficult to understand the healing process. A computerized search using relevant search terms was performed in the PubMed, EMBASE, Scopus, and Cochrane Library databases, as well as a manual search of reference lists. Searches were limited to studies that investigated tendon graft healing to bone by histologic examination after anterior cruciate ligament (ACL) reconstruction with hamstring. Ten studies were determined to be eligible for this systematic review. Thirty-seven cases were extracted from the included studies. Most studies showed that a fibrovascular interface would form at the tendon-bone interface at the early stage and a fibrous indirect interface with Sharpey-like fibers would be expected at the later stage. Cartilage-like tissue at tendon graft-bone interface was reported in three studies. Tendon graft failed to integrate with the surrounding bone in 10 of the 37 cases. Unexpectedly, suspensory type of fixation was used for the above failure cases. An indirect type of insertion with Sharpey-like fibers at tendon-bone interface could be expected after ACL reconstruction with hamstring. Regional cartilage-like tissue may form at tendon-bone interface occasionally. The underlying tendon-to-bone healing process is far from understood in the human hamstring ACL reconstruction. Further human studies are highly needed to understand tendon graft healing in bone tunnel after hamstring ACL reconstruction. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

A Question of Interface Design: How Do Online Service GUIs Measure Up?

ERIC Educational Resources Information Center

Head, Alison J.

1997-01-01

Describes recent improvements in graphical user interfaces (GUIs) offered by online services. Highlights include design considerations, including computer engineering capabilities and users' abilities; fundamental GUI design principles; user empowerment; visual communication and interaction; and an evaluation of online search interfaces. (LRW)

Tags Extarction from Spatial Documents in Search Engines

NASA Astrophysics Data System (ADS)

Borhaninejad, S.; Hakimpour, F.; Hamzei, E.

2015-12-01

Nowadays the selective access to information on the Web is provided by search engines, but in the cases which the data includes spatial information the search task becomes more complex and search engines require special capabilities. The purpose of this study is to extract the information which lies in spatial documents. To that end, we implement and evaluate information extraction from GML documents and a retrieval method in an integrated approach. Our proposed system consists of three components: crawler, database and user interface. In crawler component, GML documents are discovered and their text is parsed for information extraction; storage. The database component is responsible for indexing of information which is collected by crawlers. Finally the user interface component provides the interaction between system and user. We have implemented this system as a pilot system on an Application Server as a simulation of Web. Our system as a spatial search engine provided searching capability throughout the GML documents and thus an important step to improve the efficiency of search engines has been taken.

HTTP-based Search and Ordering Using ECHO's REST-based and OpenSearch APIs

NASA Astrophysics Data System (ADS)

Baynes, K.; Newman, D. J.; Pilone, D.

2012-12-01

Metadata is an important entity in the process of cataloging, discovering, and describing Earth science data. NASA's Earth Observing System (EOS) ClearingHOuse (ECHO) acts as the core metadata repository for EOSDIS data centers, providing a centralized mechanism for metadata and data discovery and retrieval. By supporting both the ESIP's Federated Search API and its own search and ordering interfaces, ECHO provides multiple capabilities that facilitate ease of discovery and access to its ever-increasing holdings. Users are able to search and export metadata in a variety of formats including ISO 19115, json, and ECHO10. This presentation aims to inform technically savvy clients interested in automating search and ordering of ECHO's metadata catalog. The audience will be introduced to practical and applicable examples of end-to-end workflows that demonstrate finding, sub-setting and ordering data that is bound by keyword, temporal and spatial constraints. Interaction with the ESIP OpenSearch Interface will be highlighted, as will ECHO's own REST-based API.

JAIL: a structure-based interface library for macromolecules.

PubMed

Günther, Stefan; von Eichborn, Joachim; May, Patrick; Preissner, Robert

2009-01-01

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular interfaces, those between interacting protein domains, interfaces of different protein chains and interfaces between proteins and nucleic acids. This results in a total number of about 184,000 database entries. All the interfaces can easily be identified by a detailed search form or by a hierarchical tree that describes the protein domain architectures classified by the SCOP database. Visual inspection of the interfaces is possible via an interactive protein viewer. Furthermore, large scale analyses are supported by an implemented sequential and by a structural clustering. Similar interfaces as well as non-redundant interfaces can be easily picked out. Additionally, the sequential conservation of binding sites was also included in the database and is retrievable via Jmol. A comprehensive download section allows the composition of representative data sets with user defined parameters. The huge data set in combination with various search options allow a comprehensive view on all interfaces between macromolecules included in the Protein Data Bank (PDB). The download of the data sets supports numerous further investigations in macromolecular recognition. JAIL is publicly available at http://bioinformatics.charite.de/jail.

Simple two-electrode biosignal amplifier.

PubMed

Dobrev, D; Neycheva, T; Mudrov, N

2005-11-01

A simple, cost effective circuit for a two-electrode non-differential biopotential amplifier is proposed. It uses a 'virtual ground' transimpedance amplifier and a parallel RC network for input common mode current equalisation, while the signal input impedance preserves its high value. With this innovative interface circuit, a simple non-inverting amplifier fully emulates high CMRR differential. The amplifier equivalent CMRR (typical range from 70-100 dB) is equal to the open loop gain of the operational amplifier used in the transimpedance interface stage. The circuit has very simple structure and utilises a small number of popular components. The amplifier is intended for use in various two-electrode applications, such as Holter-type monitors, defibrillators, ECG monitors, biotelemetry devices etc.

CNVinspector: a web-based tool for the interactive evaluation of copy number variations in single patients and in cohorts.

PubMed

Knierim, Ellen; Schwarz, Jana Marie; Schuelke, Markus; Seelow, Dominik

2013-08-01

Many genetic disorders are caused by copy number variations (CNVs) in the human genome. However, the large number of benign CNV polymorphisms makes it difficult to delineate causative variants for a certain disease phenotype. Hence, we set out to create software that accumulates and visualises locus-specific knowledge and enables clinicians to study their own CNVs in the context of known polymorphisms and disease variants. CNV data from healthy cohorts (Database of Genomic Variants) and from disease-related databases (DECIPHER) were integrated into a joint resource. Data are presented in an interactive web-based application that allows inspection, evaluation and filtering of CNVs in single individuals or in entire cohorts. CNVinspector provides simple interfaces to upload CNV data, compare them with own or published control data and visualise the results in graphical interfaces. Beyond choosing control data from different public studies, platforms and methods, dedicated filter options allow the detection of CNVs that are either enriched in patients or depleted in controls. Alternatively, a search can be restricted to those CNVs that appear in individuals of similar clinical phenotype. For each gene of interest within a CNV, we provide a link to NCBI, ENSEMBL and the GeneDistiller search engine to browse for potential disease-associated genes. With its user-friendly handling, the integration of control data and the filtering options, CNVinspector will facilitate the daily work of clinical geneticists and accelerate the delineation of new syndromes and gene functions. CNVinspector is freely accessible under http://www.cnvinspector.org.

Visualization of usability and functionality of a professional website through web-mining.

PubMed

Jones, Josette F; Mahoui, Malika; Gopa, Venkata Devi Pragna

2007-10-11

Functional interface design requires understanding of the information system structure and the user. Web logs record user interactions with the interface, and thus provide some insight into user search behavior and efficiency of the search process. The present study uses a data-mining approach with techniques such as association rules, clustering and classification, to visualize the usability and functionality of a digital library through in depth analyses of web logs.

CodeSlinger: a case study in domain-driven interactive tool design for biomedical coding scheme exploration and use.

PubMed

Flowers, Natalie L

2010-01-01

CodeSlinger is a desktop application that was developed to aid medical professionals in the intertranslation, exploration, and use of biomedical coding schemes. The application was designed to provide a highly intuitive, easy-to-use interface that simplifies a complex business problem: a set of time-consuming, laborious tasks that were regularly performed by a group of medical professionals involving manually searching coding books, searching the Internet, and checking documentation references. A workplace observation session with a target user revealed the details of the current process and a clear understanding of the business goals of the target user group. These goals drove the design of the application's interface, which centers on searches for medical conditions and displays the codes found in the application's database that represent those conditions. The interface also allows the exploration of complex conceptual relationships across multiple coding schemes.

Patient-Centered Tools for Medication Information Search

PubMed Central

Wilcox, Lauren; Feiner, Steven; Elhadad, Noémie; Vawdrey, David; Tran, Tran H.

2016-01-01

Recent research focused on online health information seeking highlights a heavy reliance on general-purpose search engines. However, current general-purpose search interfaces do not necessarily provide adequate support for non-experts in identifying suitable sources of health information. Popular search engines have recently introduced search tools in their user interfaces for a range of topics. In this work, we explore how such tools can support non-expert, patient-centered health information search. Scoping the current work to medication-related search, we report on findings from a formative study focused on the design of patient-centered, medication-information search tools. Our study included qualitative interviews with patients, family members, and domain experts, as well as observations of their use of Remedy, a technology probe embodying a set of search tools. Post-operative cardiothoracic surgery patients and their visiting family members used the tools to find information about their hospital medications and were interviewed before and after their use. Domain experts conducted similar search tasks and provided qualitative feedback on their preferences and recommendations for designing these tools. Findings from our study suggest the importance of four valuation principles underlying our tools: credibility, readability, consumer perspective, and topical relevance. PMID:28163972

Patient-Centered Tools for Medication Information Search.

PubMed

Wilcox, Lauren; Feiner, Steven; Elhadad, Noémie; Vawdrey, David; Tran, Tran H

2014-05-20

Recent research focused on online health information seeking highlights a heavy reliance on general-purpose search engines. However, current general-purpose search interfaces do not necessarily provide adequate support for non-experts in identifying suitable sources of health information. Popular search engines have recently introduced search tools in their user interfaces for a range of topics. In this work, we explore how such tools can support non-expert, patient-centered health information search. Scoping the current work to medication-related search, we report on findings from a formative study focused on the design of patient-centered, medication-information search tools. Our study included qualitative interviews with patients, family members, and domain experts, as well as observations of their use of Remedy, a technology probe embodying a set of search tools. Post-operative cardiothoracic surgery patients and their visiting family members used the tools to find information about their hospital medications and were interviewed before and after their use. Domain experts conducted similar search tasks and provided qualitative feedback on their preferences and recommendations for designing these tools. Findings from our study suggest the importance of four valuation principles underlying our tools: credibility, readability, consumer perspective, and topical relevance.

BioSearch: a semantic search engine for Bio2RDF

PubMed Central

Qiu, Honglei; Huang, Jiacheng

2017-01-01

Abstract Biomedical data are growing at an incredible pace and require substantial expertise to organize data in a manner that makes them easily findable, accessible, interoperable and reusable. Massive effort has been devoted to using Semantic Web standards and technologies to create a network of Linked Data for the life sciences, among others. However, while these data are accessible through programmatic means, effective user interfaces for non-experts to SPARQL endpoints are few and far between. Contributing to user frustrations is that data are not necessarily described using common vocabularies, thereby making it difficult to aggregate results, especially when distributed across multiple SPARQL endpoints. We propose BioSearch — a semantic search engine that uses ontologies to enhance federated query construction and organize search results. BioSearch also features a simplified query interface that allows users to optionally filter their keywords according to classes, properties and datasets. User evaluation demonstrated that BioSearch is more effective and usable than two state of the art search and browsing solutions. Database URL: http://ws.nju.edu.cn/biosearch/ PMID:29220451

Publishing NASA Metadata as Linked Open Data for Semantic Mashups

NASA Astrophysics Data System (ADS)

Wilson, Brian; Manipon, Gerald; Hua, Hook

2014-05-01

Data providers are now publishing more metadata in more interoperable forms, e.g. Atom or RSS 'casts', as Linked Open Data (LOD), or as ISO Metadata records. A major effort on the part of the NASA's Earth Science Data and Information System (ESDIS) project is the aggregation of metadata that enables greater data interoperability among scientific data sets regardless of source or application. Both the Earth Observing System (EOS) ClearingHOuse (ECHO) and the Global Change Master Directory (GCMD) repositories contain metadata records for NASA (and other) datasets and provided services. These records contain typical fields for each dataset (or software service) such as the source, creation date, cognizant institution, related access URL's, and domain and variable keywords to enable discovery. Under a NASA ACCESS grant, we demonstrated how to publish the ECHO and GCMD dataset and services metadata as LOD in the RDF format. Both sets of metadata are now queryable at SPARQL endpoints and available for integration into "semantic mashups" in the browser. It is straightforward to reformat sets of XML metadata, including ISO, into simple RDF and then later refine and improve the RDF predicates by reusing known namespaces such as Dublin core, georss, etc. All scientific metadata should be part of the LOD world. In addition, we developed an "instant" drill-down and browse interface that provides faceted navigation so that the user can discover and explore the 25,000 datasets and 3000 services. The available facets and the free-text search box appear in the left panel, and the instantly updated results for the dataset search appear in the right panel. The user can constrain the value of a metadata facet simply by clicking on a word (or phrase) in the "word cloud" of values for each facet. The display section for each dataset includes the important metadata fields, a full description of the dataset, potentially some related URL's, and a "search" button that points to an OpenSearch GUI that is pre-configured to search for granules within the dataset. We will present our experiences with converting NASA metadata into LOD, discuss the challenges, illustrate some of the enabled mashups, and demonstrate the latest version of the "instant browse" interface for navigating multiple metadata collections.

SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor.

PubMed

de Man, Tom J B; Limbago, Brandi M

2016-01-01

We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the database is initially populated from a public repository of acquired resistance determinants (i.e., ARG-ANNOT), it can be customized for particular pathogen groups and resistance mechanisms. For instance, outer membrane porin sequences associated with carbapenem resistance phenotypes can be added, and known intrinsic mechanisms can be included. Unique about this tool is the ability to easily detect putative new alleles and truncated versions of existing AR genes. Variants and potential new alleles are brought to the attention of the user for further investigation. For instance, SSTAR is able to identify modified or truncated versions of porins, which may be of great importance in carbapenemase-negative carbapenem-resistant Enterobacteriaceae. SSTAR is written in Java and is therefore platform independent and compatible with both Windows and Unix operating systems. SSTAR and its manual, which includes a simple installation guide, are freely available from https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR-. IMPORTANCE Whole-genome sequencing (WGS) is quickly becoming a routine method for identifying genes associated with antimicrobial resistance (AR). However, for many microbiologists, the use and analysis of WGS data present a substantial challenge. We developed SSTAR, software with a graphical user interface that enables the identification of known AR genes from WGS and has the unique capacity to easily detect new variants of known AR genes, including truncated protein variants. Current software solutions do not notify the user when genes are truncated and, therefore, likely nonfunctional, which makes phenotype predictions less accurate. SSTAR users can apply any AR database of interest as a reference comparator and can manually add genes that impact resistance, even if such genes are not resistance determinants per se (e.g., porins and efflux pumps).

Variations in Medical Subject Headings (MeSH) mapping: from the natural language of patron terms to the controlled vocabulary of mapped lists*

PubMed Central

Gault, Lora V.; Shultz, Mary; Davies, Kathy J.

2002-01-01

Objectives: This study compared the mapping of natural language patron terms to the Medical Subject Headings (MeSH) across six MeSH interfaces for the MEDLINE database. Methods: Test data were obtained from search requests submitted by patrons to the Library of the Health Sciences, University of Illinois at Chicago, over a nine-month period. Search request statements were parsed into separate terms or phrases. Using print sources from the National Library of Medicine, Each parsed patron term was assigned corresponding MeSH terms. Each patron term was entered into each of the selected interfaces to determine how effectively they mapped to MeSH. Data were collected for mapping success, accessibility of MeSH term within mapped list, and total number of MeSH choices within each list. Results: The selected MEDLINE interfaces do not map the same patron term in the same way, nor do they consistently lead to what is considered the appropriate MeSH term. Conclusions: If searchers utilize the MEDLINE database to its fullest potential by mapping to MeSH, the results of the mapping will vary between interfaces. This variance may ultimately impact the search results. These differences should be considered when choosing a MEDLINE interface and when instructing end users. PMID:11999175

Variations in Medical Subject Headings (MeSH) mapping: from the natural language of patron terms to the controlled vocabulary of mapped lists.

PubMed

Gault, Lora V; Shultz, Mary; Davies, Kathy J

2002-04-01

This study compared the mapping of natural language patron terms to the Medical Subject Headings (MeSH) across six MeSH interfaces for the MEDLINE database. Test data were obtained from search requests submitted by patrons to the Library of the Health Sciences, University of Illinois at Chicago, over a nine-month period. Search request statements were parsed into separate terms or phrases. Using print sources from the National Library of Medicine, Each parsed patron term was assigned corresponding MeSH terms. Each patron term was entered into each of the selected interfaces to determine how effectively they mapped to MeSH. Data were collected for mapping success, accessibility of MeSH term within mapped list, and total number of MeSH choices within each list. The selected MEDLINE interfaces do not map the same patron term in the same way, nor do they consistently lead to what is considered the appropriate MeSH term. If searchers utilize the MEDLINE database to its fullest potential by mapping to MeSH, the results of the mapping will vary between interfaces. This variance may ultimately impact the search results. These differences should be considered when choosing a MEDLINE interface and when instructing end users.

Interfaces and Expert Systems for Online Retrieval.

ERIC Educational Resources Information Center

Kehoe, Cynthia A.

1985-01-01

This paper reviews the history of separate online system interfaces which led to efforts to develop expert systems for searching databases, particularly for end users, and introduces the research on such expert systems. Appended is a bibliography of sources on interfaces and expert systems for online retrieval. (Author/EJS)

Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications.

MusiCat System Makes Library Searches More Fruitful.

ERIC Educational Resources Information Center

Hansen, Per Hofman

2002-01-01

Describes MusiCat, an experimental user interface designed in Denmark that reflects the different ways that patrons think when searching for musical material on the Web. Discusses technology versus content; search trees that use a hierarchy of subject terms; and usability testing. (LRW)

The Perfectly Organized Search Service.

ERIC Educational Resources Information Center

Leach, Sandra Sinsel; Spencer, Mary Ellen

1993-01-01

Describes the evolution and operation of the successful Database Search Service (DSS) at the John C. Hodges Library, University of Tennessee, with detailed information about equipment, policies, software, training, and physical layout. Success is attributed to careful administration, standardization of search equipment and interfaces, staff…

Testing search strategies for systematic reviews in the Medline literature database through PubMed.

PubMed

Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

2014-04-01

A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

Global trends in infectious diseases at the wildlife-livestock interface.

PubMed

Wiethoelter, Anke K; Beltrán-Alcrudo, Daniel; Kock, Richard; Mor, Siobhan M

2015-08-04

The role and significance of wildlife-livestock interfaces in disease ecology has largely been neglected, despite recent interest in animals as origins of emerging diseases in humans. Scoping review methods were applied to objectively assess the relative interest by the scientific community in infectious diseases at interfaces between wildlife and livestock, to characterize animal species and regions involved, as well as to identify trends over time. An extensive literature search combining wildlife, livestock, disease, and geographical search terms yielded 78,861 publications, of which 15,998 were included in the analysis. Publications dated from 1912 to 2013 and showed a continuous increasing trend, including a shift from parasitic to viral diseases over time. In particular there was a significant increase in publications on the artiodactyls-cattle and bird-poultry interface after 2002 and 2003, respectively. These trends could be traced to key disease events that stimulated public interest and research funding. Among the top 10 diseases identified by this review, the majority were zoonoses. Prominent wildlife-livestock interfaces resulted largely from interaction between phylogenetically closely related and/or sympatric species. The bird-poultry interface was the most frequently cited wildlife-livestock interface worldwide with other interfaces reflecting regional circumstances. This review provides the most comprehensive overview of research on infectious diseases at the wildlife-livestock interface to date.

Global trends in infectious diseases at the wildlife–livestock interface

PubMed Central

Wiethoelter, Anke K.; Beltrán-Alcrudo, Daniel; Kock, Richard; Mor, Siobhan M.

2015-01-01

The role and significance of wildlife–livestock interfaces in disease ecology has largely been neglected, despite recent interest in animals as origins of emerging diseases in humans. Scoping review methods were applied to objectively assess the relative interest by the scientific community in infectious diseases at interfaces between wildlife and livestock, to characterize animal species and regions involved, as well as to identify trends over time. An extensive literature search combining wildlife, livestock, disease, and geographical search terms yielded 78,861 publications, of which 15,998 were included in the analysis. Publications dated from 1912 to 2013 and showed a continuous increasing trend, including a shift from parasitic to viral diseases over time. In particular there was a significant increase in publications on the artiodactyls–cattle and bird–poultry interface after 2002 and 2003, respectively. These trends could be traced to key disease events that stimulated public interest and research funding. Among the top 10 diseases identified by this review, the majority were zoonoses. Prominent wildlife–livestock interfaces resulted largely from interaction between phylogenetically closely related and/or sympatric species. The bird–poultry interface was the most frequently cited wildlife–livestock interface worldwide with other interfaces reflecting regional circumstances. This review provides the most comprehensive overview of research on infectious diseases at the wildlife–livestock interface to date. PMID:26195733

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

PubMed Central

2015-01-01

As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes. PMID:24830957

Human Interface to Netcentricity

DTIC Science & Technology

2006-06-01

experiencing. This is a radically different approach than using a federated search engine to bring back all relevant documents. The search engine...not be any closer to answering their question. More importantly, if they only have access to a 22 federated search , the program does not have the

Content-based Music Search and Recommendation System

NASA Astrophysics Data System (ADS)

Takegawa, Kazuki; Hijikata, Yoshinori; Nishida, Shogo

Recently, the turn volume of music data on the Internet has increased rapidly. This has increased the user's cost to find music data suiting their preference from such a large data set. We propose a content-based music search and recommendation system. This system has an interface for searching and finding music data and an interface for editing a user profile which is necessary for music recommendation. By exploiting the visualization of the feature space of music and the visualization of the user profile, the user can search music data and edit the user profile. Furthermore, by exploiting the infomation which can be acquired from each visualized object in a mutually complementary manner, we make it easier for the user to search music data and edit the user profile. Concretely, the system gives to the user an information obtained from the user profile when searching music data and an information obtained from the feature space of music when editing the user profile.

Toward a human-centered hyperlipidemia management system: the interaction between internal and external information on relational data search.

PubMed

Gong, Yang; Zhang, Jiajie

2011-04-01

In a distributed information search task, data representation and cognitive distribution jointly affect user search performance in terms of response time and accuracy. Guided by UFuRT (User, Function, Representation, Task), a human-centered framework, we proposed a search model and task taxonomy. The model defines its application in the context of healthcare setting. The taxonomy clarifies the legitimate operations for each type of search task of relational data. We then developed experimental prototypes of hyperlipidemia data displays. Based on the displays, we tested the search tasks performance through two experiments. The experiments are of a within-subject design with a random sample of 24 participants. The results support our hypotheses and validate the prediction of the model and task taxonomy. In this study, representation dimensions, data scales, and search task types are the main factors in determining search efficiency and effectiveness. Specifically, the more external representations provided on the interface the better search task performance of users. The results also suggest the ideal search performance occurs when the question type and its corresponding data scale representation match. The implications of the study lie in contributing to the effective design of search interface for relational data, especially laboratory results, which could be more effectively designed in electronic medical records.

The DIMA web resource--exploring the protein domain network.

PubMed

Pagel, Philipp; Oesterheld, Matthias; Stümpflen, Volker; Frishman, Dmitrij

2006-04-15

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

A universal preconditioner for simulating condensed phase materials

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

Packwood, David; Ortner, Christoph, E-mail: c.ortner@warwick.ac.uk; Kermode, James, E-mail: j.r.kermode@warwick.ac.uk

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor ofmore » two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.« less

Seamless presentation capture, indexing, and management

NASA Astrophysics Data System (ADS)

Hilbert, David M.; Cooper, Matthew; Denoue, Laurent; Adcock, John; Billsus, Daniel

2005-10-01

Technology abounds for capturing presentations. However, no simple solution exists that is completely automatic. ProjectorBox is a "zero user interaction" appliance that automatically captures, indexes, and manages presentation multimedia. It operates continuously to record the RGB information sent from presentation devices, such as a presenter's laptop, to display devices, such as a projector. It seamlessly captures high-resolution slide images, text and audio. It requires no operator, specialized software, or changes to current presentation practice. Automatic media analysis is used to detect presentation content and segment presentations. The analysis substantially enhances the web-based user interface for browsing, searching, and exporting captured presentations. ProjectorBox has been in use for over a year in our corporate conference room, and has been deployed in two universities. Our goal is to develop automatic capture services that address both corporate and educational needs.

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

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

Cottam, Joseph A.; Blaha, Leslie M.

Systems have biases. Their interfaces naturally guide a user toward specific patterns of action. For example, modern word-processors and spreadsheets are both capable of taking word wrapping, checking spelling, storing tables, and calculating formulas. You could write a paper in a spreadsheet or could do simple business modeling in a word-processor. However, their interfaces naturally communicate which function they are designed for. Visual analytic interfaces also have biases. In this paper, we outline why simple Markov models are a plausible tool for investigating that bias and how they might be applied. We also discuss some anticipated difficulties in such modelingmore » and touch briefly on what some Markov model extensions might provide.« less

Navigation interface for recommending home medical products.

PubMed

Luo, Gang

2012-04-01

Based on users' health issues, an intelligent personal health record (iPHR) system can automatically recommend home medical products (HMPs) and display them in a sequential order. However, the sequential output interface does not categorize search results and is not easy for users to quickly navigate to their desired HMPs. To address this problem, we developed a navigation interface for retrieved HMPs. Our idea is to use medical knowledge and nursing knowledge to construct a navigation hierarchy based on product categories. This hierarchy is added to the left side of each search result Web page to help users move through retrieved HMPs. We demonstrate the effectiveness of our techniques using USMLE medical exam cases.

Omicseq: a web-based search engine for exploring omics datasets.

PubMed

Sun, Xiaobo; Pittard, William S; Xu, Tianlei; Chen, Li; Zwick, Michael E; Jiang, Xiaoqian; Wang, Fusheng; Qin, Zhaohui S

2017-07-03

The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve 'findability' of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Improved Targeting Through Collaborative Decision-Making and Brain Computer Interfaces

NASA Technical Reports Server (NTRS)

Stoica, Adrian; Barrero, David F.; McDonald-Maier, Klaus

2013-01-01

This paper reports a first step toward a brain-computer interface (BCI) for collaborative targeting. Specifically, we explore, from a broad perspective, how the collaboration of a group of people can increase the performance on a simple target identification task. To this end, we requested a group of people to identify the location and color of a sequence of targets appearing on the screen and measured the time and accuracy of the response. The individual results are compared to a collective identification result determined by simple majority voting, with random choice in case of drawn. The results are promising, as the identification becomes significantly more reliable even with this simple voting and a small number of people (either odd or even number) involved in the decision. In addition, the paper briefly analyzes the role of brain-computer interfaces in collaborative targeting, extending the targeting task by using a BCI instead of a mechanical response.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Sirius PSB: a generic system for analysis of biological sequences.

PubMed

Koh, Chuan Hock; Lin, Sharene; Jedd, Gregory; Wong, Limsoon

2009-12-01

Computational tools are essential components of modern biological research. For example, BLAST searches can be used to identify related proteins based on sequence homology, or when a new genome is sequenced, prediction models can be used to annotate functional sites such as transcription start sites, translation initiation sites and polyadenylation sites and to predict protein localization. Here we present Sirius Prediction Systems Builder (PSB), a new computational tool for sequence analysis, classification and searching. Sirius PSB has four main operations: (1) Building a classifier, (2) Deploying a classifier, (3) Search for proteins similar to query proteins, (4) Preliminary and post-prediction analysis. Sirius PSB supports all these operations via a simple and interactive graphical user interface. Besides being a convenient tool, Sirius PSB has also introduced two novelties in sequence analysis. Firstly, genetic algorithm is used to identify interesting features in the feature space. Secondly, instead of the conventional method of searching for similar proteins via sequence similarity, we introduced searching via features' similarity. To demonstrate the capabilities of Sirius PSB, we have built two prediction models - one for the recognition of Arabidopsis polyadenylation sites and another for the subcellular localization of proteins. Both systems are competitive against current state-of-the-art models based on evaluation of public datasets. More notably, the time and effort required to build each model is greatly reduced with the assistance of Sirius PSB. Furthermore, we show that under certain conditions when BLAST is unable to find related proteins, Sirius PSB can identify functionally related proteins based on their biophysical similarities. Sirius PSB and its related supplements are available at: http://compbio.ddns.comp.nus.edu.sg/~sirius.

Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

Constructing Effective Search Strategies for Electronic Searching.

ERIC Educational Resources Information Center

Flanagan, Lynn; Parente, Sharon Campbell

Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

Research on Agriculture Domain Meta-Search Engine System

NASA Astrophysics Data System (ADS)

Xie, Nengfu; Wang, Wensheng

The rapid growth of agriculture web information brings a fact that search engine can not return a satisfied result for users’ queries. In this paper, we propose an agriculture domain search engine system, called ADSE, that can obtains results by an advance interface to several searches and aggregates them. We also discuss two key technologies: agriculture information determination and engine.

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

US Search and Rescue Mission Control Center functions

NASA Technical Reports Server (NTRS)

1977-01-01

A satellite aided Search and Rescue (SAR) Mission concept consisting of a local coverage bent pipe system, and a global coverage system is described. The SAR instrument is to consist of a Canadian repeater and a French processor for which Canada and France, respectively are to evaluate health and trends. Performance evaluations of each system were provided. The United States and Canada will each have a Search and Rescue Mission Control Center (MCC) and their functions were also examined. A summary of the interface requirements necessary to perform each function was included as well as the information requirements between the USMCC and each of its interfaces. Physical requirements such as location, manning etc. of the USMCC were discussed.

Adaptive interface for personalizing information seeking.

PubMed

Narayanan, S; Koppaka, Lavanya; Edala, Narasimha; Loritz, Don; Daley, Raymond

2004-12-01

An adaptive interface autonomously adjusts its display and available actions to current goals and abilities of the user by assessing user status, system task, and the context. Knowledge content adaptability is needed for knowledge acquisition and refinement tasks. In the case of knowledge content adaptability, the requirements of interface design focus on the elicitation of information from the user and the refinement of information based on patterns of interaction. In such cases, the emphasis on adaptability is on facilitating information search and knowledge discovery. In this article, we present research on adaptive interfaces that facilitates personalized information seeking from a large data warehouse. The resulting proof-of-concept system, called source recommendation system (SRS), assists users in locating and navigating data sources in the repository. Based on the initial user query and an analysis of the content of the search results, the SRS system generates a profile of the user tailored to the individual's context during information seeking. The user profiles are refined successively and are used in progressively guiding the user to the appropriate set of sources within the knowledge base. The SRS system is implemented as an Internet browser plug-in to provide a seamless and unobtrusive, personalized experience to the users during the information search process. The rationale behind our approach, system design, empirical evaluation, and implications for research on adaptive interfaces are described in this paper.

78 FR 35761 - Final Priority; National Institute on Disability and Rehabilitation Research-Disability and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-14

... include cloud computing applications that allow for personalized accessible interfaces. The RERC must... the article search feature at: www.federalregister.gov . Specifically, through the advanced search...

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

WORDGRAPH: Keyword-in-Context Visualization for NETSPEAK's Wildcard Search.

PubMed

Riehmann, Patrick; Gruendl, Henning; Potthast, Martin; Trenkmann, Martin; Stein, Benno; Froehlich, Benno

2012-09-01

The WORDGRAPH helps writers in visually choosing phrases while writing a text. It checks for the commonness of phrases and allows for the retrieval of alternatives by means of wildcard queries. To support such queries, we implement a scalable retrieval engine, which returns high-quality results within milliseconds using a probabilistic retrieval strategy. The results are displayed as WORDGRAPH visualization or as a textual list. The graphical interface provides an effective means for interactive exploration of search results using filter techniques, query expansion, and navigation. Our observations indicate that, of three investigated retrieval tasks, the textual interface is sufficient for the phrase verification task, wherein both interfaces support context-sensitive word choice, and the WORDGRAPH best supports the exploration of a phrase's context or the underlying corpus. Our user study confirms these observations and shows that WORDGRAPH is generally the preferred interface over the textual result list for queries containing multiple wildcards.

Lessons learned from an Ada conversion project

NASA Technical Reports Server (NTRS)

Porter, Tim

1988-01-01

Background; SAVVAS architecture; software portability; history of Ada; isolation of non-portable code; simple terminal interface package; constraints of language features; and virtual interfaces are outlined. This presentation is represented by viewgraphs only.

Concurrent Image Processing Executive (CIPE). Volume 3: User's guide

NASA Technical Reports Server (NTRS)

Lee, Meemong; Cooper, Gregory T.; Groom, Steven L.; Mazer, Alan S.; Williams, Winifred I.; Kong, Mih-Seh

1990-01-01

CIPE (the Concurrent Image Processing Executive) is both an executive which organizes the parameter inputs for hypercube applications and an environment which provides temporary data workspace and simple real-time function definition facilities for image analysis. CIPE provides two types of user interface. The Command Line Interface (CLI) provides a simple command-driven environment allowing interactive function definition and evaluation of algebraic expressions. The menu interface employs a hierarchical screen-oriented menu system where the user is led through a menu tree to any specific application and then given a formatted panel screen for parameter entry. How to initialize the system through the setup function, how to read data into CIPE symbols, how to manipulate and display data through the use of executive functions, and how to run an application in either user interface mode, are described.

Positron studies of metal-oxide-semiconductor structures

NASA Astrophysics Data System (ADS)

Au, H. L.; Asoka-Kumar, P.; Nielsen, B.; Lynn, K. G.

1993-03-01

Positron annihilation spectroscopy provides a new probe to study the properties of interface traps in metal-oxide semiconductors (MOS). Using positrons, we have examined the behavior of the interface traps as a function of gate bias. We propose a simple model to explain the positron annihilation spectra from the interface region of a MOS capacitor.

An Accessible User Interface for Geoscience and Programming

NASA Astrophysics Data System (ADS)

Sevre, E. O.; Lee, S.

2012-12-01

The goal of this research is to develop an interface that will simplify user interaction with software for scientists. The motivating factor of the research is to develop tools that assist scientists with limited motor skills with the efficient generation and use of software tools. Reliance on computers and programming is increasing in the world of geology, and it is increasingly important for geologists and geophysicists to have the computational resources to use advanced software and edit programs for their research. I have developed a prototype of a program to help geophysicists write programs using a simple interface that requires only simple single-mouse-clicks to input code. It is my goal to minimize the amount of typing necessary to create simple programs and scripts to increase accessibility for people with disabilities limiting fine motor skills. This interface can be adapted for various programming and scripting languages. Using this interface will simplify development of code for C/C++, Java, and GMT, and can be expanded to support any other text based programming language. The interface is designed around the concept of maximizing the amount of code that can be written using a minimum number of clicks and typing. The screen is split into two sections: a list of click-commands is on the left hand side, and a text area is on the right hand side. When the user clicks on a command on the left hand side the applicable code is automatically inserted at the insertion point in the text area. Currently in the C/C++ interface, there are commands for common code segments that are often used, such as for loops, comments, print statements, and structured code creation. The primary goal is to provide an interface that will work across many devices for developing code. A simple prototype has been developed for the iPad. Due to the limited number of devices that an iOS application can be used with, the code has been re-written in Java to run on a wider range of devices. Currently, the software works in a prototype mode, and it is our goal to further development to create software that can benefit a wide range of people working in geosciences, which will make code development practical and accessible for a wider audience of scientists. By using an interface like this, it reduces potential for errors by reusing known working code.

Visual Exploratory Search of Relationship Graphs on Smartphones

PubMed Central

Ouyang, Jianquan; Zheng, Hao; Kong, Fanbin; Liu, Tianming

2013-01-01

This paper presents a novel framework for Visual Exploratory Search of Relationship Graphs on Smartphones (VESRGS) that is composed of three major components: inference and representation of semantic relationship graphs on the Web via meta-search, visual exploratory search of relationship graphs through both querying and browsing strategies, and human-computer interactions via the multi-touch interface and mobile Internet on smartphones. In comparison with traditional lookup search methodologies, the proposed VESRGS system is characterized with the following perceived advantages. 1) It infers rich semantic relationships between the querying keywords and other related concepts from large-scale meta-search results from Google, Yahoo! and Bing search engines, and represents semantic relationships via graphs; 2) the exploratory search approach empowers users to naturally and effectively explore, adventure and discover knowledge in a rich information world of interlinked relationship graphs in a personalized fashion; 3) it effectively takes the advantages of smartphones’ user-friendly interfaces and ubiquitous Internet connection and portability. Our extensive experimental results have demonstrated that the VESRGS framework can significantly improve the users’ capability of seeking the most relevant relationship information to their own specific needs. We envision that the VESRGS framework can be a starting point for future exploration of novel, effective search strategies in the mobile Internet era. PMID:24223936

Llnking the EarthScope Data Virtual Catalog to the GEON Portal

NASA Astrophysics Data System (ADS)

Lin, K.; Memon, A.; Baru, C.

2008-12-01

The EarthScope Data Portal provides a unified, single-point of access to EarthScope data and products from USArray, Plate Boundary Observatory (PBO), and San Andreas Fault Observatory at Depth (SAFOD) experiments. The portal features basic search and data access capabilities to allow users to discover and access EarthScope data using spatial, temporal, and other metadata-based (data type, station specific) search conditions. The portal search module is the user interface implementation of the EarthScope Data Search Web Service. This Web Service acts as a virtual catalog that in turn invokes Web services developed by IRIS (Incorporated Research Institutions for Seismology), UNAVCO (University NAVSTAR Consortium), and GFZ (German Research Center for Geosciences) to search for EarthScope data in the archives at each of these locations. These Web Services provide information about all resources (data) that match the specified search conditions. In this presentation we will describe how the EarthScope Data Search Web service can be integrated into the GEONsearch application in the GEON Portal (see http://portal.geongrid.org). Thus, a search request issued at the GEON Portal will also search the EarthScope virtual catalog thereby providing users seamless access to data in GEON as well as the Earthscope via a common user interface.

Database Search Engines: Paradigms, Challenges and Solutions.

PubMed

Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

A Simple Inexpensive Bridgman-Stockbarger Crystal Growth System for Organic Materials

NASA Technical Reports Server (NTRS)

Choi, J.; Aggarwal, M. D.; Wang, W. S.; Metzl, R.; Bhat, K.; Penn, Benjamin G.; Frazier, Donald O.

1996-01-01

Direct observation of solid-liquid interface is important for the directional solidification to determine the desired interface shape by controlling the growth parameters. To grow good quality single crystals of novel organic nonlinear optical materials, a simple inexpensive Bridgman-Stockbarger (BS) crystal growth system has been designed and fabricated. Two immiscible liquids have been utilized to create two zones for this crystal growth system. Bulk single crystals of benzil derivative and n-salicylidene-aniline have been successfully grown in this system. The optimum lowering rate has been found to be 0.1 mm/h for the flat interface. Results on the crystal growth and other parameters of the grown crystals are presented.

A Method for Automated Detection of Usability Problems from Client User Interface Events

PubMed Central

Saadawi, Gilan M.; Legowski, Elizabeth; Medvedeva, Olga; Chavan, Girish; Crowley, Rebecca S.

2005-01-01

Think-aloud usability analysis provides extremely useful data but is very time-consuming and expensive to perform because of the extensive manual video analysis that is required. We describe a simple method for automated detection of usability problems from client user interface events for a developing medical intelligent tutoring system. The method incorporates (1) an agent-based method for communication that funnels all interface events and system responses to a centralized database, (2) a simple schema for representing interface events and higher order subgoals, and (3) an algorithm that reproduces the criteria used for manual coding of usability problems. A correction factor was empirically determining to account for the slower task performance of users when thinking aloud. We tested the validity of the method by simultaneously identifying usability problems using TAU and manually computing them from stored interface event data using the proposed algorithm. All usability problems that did not rely on verbal utterances were detectable with the proposed method. PMID:16779121

Novel structure formation at the bottom surface of porous anodic alumina fabricated by single step anodization process.

PubMed

Ali, Ghafar; Ahmad, Maqsood; Akhter, Javed Iqbal; Maqbool, Muhammad; Cho, Sung Oh

2010-08-01

A simple approach for the growth of long-range highly ordered nanoporous anodic alumina film in H(2)SO(4) electrolyte through a single step anodization without any additional pre-anodizing procedure is reported. Free-standing porous anodic alumina film of 180 microm thickness with through hole morphology was obtained. A simple and single step process was used for the detachment of alumina from aluminum substrate. The effect of anodizing conditions, such as anodizing voltage and time on the pore diameter and pore ordering is discussed. The metal/oxide and oxide/electrolyte interfaces were examined by high resolution scanning transmission electron microscope. The arrangement of pores on metal/oxide interface was well ordered with smaller diameters than that of the oxide/electrolyte interface. The inter-pore distance was larger in metal/oxide interface as compared to the oxide/electrolyte interface. The size of the ordered domain was found to depend strongly upon anodizing voltage and time. (c) 2010 Elsevier Ltd. All rights reserved.

A New Interface for the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Koppers, A. A. P.; Tauxe, L.; Constable, C.; Shaar, R.; Jonestrask, L.

2014-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of uploading data, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Data uploading has been simplified and no longer requires the use of the Excel SmartBook interface. Instead, properly formatted MagIC text files can be dragged-and-dropped onto an HTML 5 web interface. Data can be uploaded one table at a time to facilitate ease of uploading and data error checking is done online on the whole dataset at once instead of incrementally in an Excel Console. Searching the database has improved with the addition of more sophisticated search parameters and with the ability to use them in complex combinations. Searches may also be saved as permanent URLs for easy reference or for use as a citation in a publication. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. Data from the MagIC database may be downloaded from individual contributions or from online searches for offline use and analysis in the tab delimited MagIC text file format. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

EMERSE: The Electronic Medical Record Search Engine

PubMed Central

Hanauer, David A.

2006-01-01

EMERSE (The Electronic Medical Record Search Engine) is an intuitive, powerful search engine for free-text documents in the electronic medical record. It offers multiple options for creating complex search queries yet has an interface that is easy enough to be used by those with minimal computer experience. EMERSE is ideal for retrospective chart reviews and data abstraction and may have potential for clinical care as well.

Design of an On-Line Query Language for Full Text Patent Search.

ERIC Educational Resources Information Center

Glantz, Richard S.

The design of an English-like query language and an interactive computer environment for searching the full text of the U.S. patent collection are discussed. Special attention is paid to achieving a transparent user interface, to providing extremely broad search capabilities (including nested substitution classes, Kleene star events, and domain…

Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

1995-01-01

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

The Influence of Gender Difference on the Information-Seeking Behaviors for the Graphical Interface of Children's Digital Library

ERIC Educational Resources Information Center

Hsieh, Tsia-ying; Wu, Ko-chiu

2015-01-01

Children conducting searches using the interfaces of library websites often encounter obstacles due to typographical errors, digital divides, or a failure to grasp keywords. Satisfaction with a given interface may also vary according to the gender of the user, making it a variable in information seeking behavior. Children benefit more from…

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.

PubMed

Jouraku, Akiya; Yamamoto, Kimiko; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Narukawa, Junko; Miyamoto, Kazuhisa; Kurita, Kanako; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Noda, Hiroaki

2013-07-09

The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM). KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers. KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target sequences such as insect resistance-related genes. KONAGAbase will be continuously updated and additional genomic/transcriptomic resources and analysis tools will be provided for further efficient analysis of the mechanism of insecticide resistance and the development of effective insecticides with a novel mode of action for DBM.

A Fast, Minimalist Search Tool for Remote Sensing Data

NASA Astrophysics Data System (ADS)

Lynnes, C. S.; Macharrie, P. G.; Elkins, M.; Joshi, T.; Fenichel, L. H.

2005-12-01

We present a tool that emphasizes speed and simplicity in searching remotely sensed Earth Science data. The tool, nicknamed "Mirador" (Spanish for a scenic overlook), provides only four freetext search form fields, for Keywords, Location, Data Start and Data Stop. This contrasts with many current Earth Science search tools that offer highly structured interfaces in order to ensure precise, non-zero results. The disadvantages of the structured approach lie in its complexity and resultant learning curve, as well as the time it takes to formulate and execute the search, thus discouraging iterative discovery. On the other hand, the success of the basic Google search interface shows that many users are willing to forgo high search precision if the search process is fast enough to enable rapid iteration. Therefore, we employ several methods to increase the speed of search formulation and execution. Search formulation is expedited by the minimalist search form, with only one required field. Also, a gazetteer enables the use of geographic terms as shorthand for latitude/longitude coordinates. The search execution is accelerated by initially presenting dataset results (returned from a Google Mini appliance) with an estimated number of "hits" for each dataset based on the user's space-time constraints. The more costly file-level search is executed against a PostGres database only when the user "drills down", and then covering only the fraction of the time period needed to return the next page of results. The simplicity of the search form makes the tool easy to learn and use, and the speed of the searches enables an iterative form of data discovery.

Rheological Properties of Natural Subduction Zone Interface: Insights from "Digital" Griggs Experiments

NASA Astrophysics Data System (ADS)

Ioannidi, P. I.; Le Pourhiet, L.; Moreno, M.; Agard, P.; Oncken, O.; Angiboust, S.

2017-12-01

The physical nature of plate locking and its relation to surface deformation patterns at different time scales (e.g. GPS displacements during the seismic cycle) can be better understood by determining the rheological parameters of the subduction interface. However, since direct rheological measurements are not possible, finite element modelling helps to determine the effective rheological parameters of the subduction interface. We used the open source finite element code pTatin to create 2D models, starting with a homogeneous medium representing shearing at the subduction interface. We tested several boundary conditions that mimic simple shear and opted for the one that best describes the Grigg's type simple shear experiments. After examining different parameters, such as shearing velocity, temperature and viscosity, we added complexity to the geometry by including a second phase. This arises from field observations, where shear zone outcrops are often composites of multiple phases: stronger crustal blocks embedded within a sedimentary and/or serpentinized matrix have been reported for several exhumed subduction zones. We implemented a simplified model to simulate simple shearing of a two-phase medium in order to quantify the effect of heterogeneous rheology on stress and strain localization. Preliminary results show different strength in the models depending on the block-to-matrix ratio. We applied our method to outcrop scale block-in-matrix geometries and by sampling at different depths along exhumed former subduction interfaces, we expect to be able to provide effective friction and viscosity of a natural interface. In a next step, these effective parameters will be used as input into seismic cycle deformation models in an attempt to assess the possible signature of field geometries on the slip behaviour of the plate interface.

User interface issues in supporting human-computer integrated scheduling

NASA Technical Reports Server (NTRS)

Cooper, Lynne P.; Biefeld, Eric W.

1991-01-01

Explored here is the user interface problems encountered with the Operations Missions Planner (OMP) project at the Jet Propulsion Laboratory (JPL). OMP uses a unique iterative approach to planning that places additional requirements on the user interface, particularly to support system development and maintenance. These requirements are necessary to support the concepts of heuristically controlled search, in-progress assessment, and iterative refinement of the schedule. The techniques used to address the OMP interface needs are given.

Implementing the Army NetCentric Data Strategy in a ServiceOriented Environment

DTIC Science & Technology

2009-04-23

D a t a D i s c o v e r y Data Retrieval Data Subscription Data Discovery D a t a A c c e s s Artifact Discovery Federated Search Data Search Data...define common interfaces to search and  retrieve data across the enterprise.  • Patterns • Search • Status • Receive – Services • Federated   Search • Artifact

The Cold Dark Matter Search test stand warm electronics card

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

Hines, Bruce; /Colorado U., Denver; Hansen, Sten

A card which does the signal processing for four SQUID amplifiers and two charge sensitive channels is described. The card performs the same functions as is presently done with two custom 9U x 280mm Eurocard modules, a commercial multi-channel VME digitizer, a PCI to GPIB interface, a PCI to VME interface and a custom built linear power supply. By integrating these functions onto a single card and using the power over Ethernet standard, the infrastructure requirements for instrumenting a Cold Dark Matter Search (CDMS) detector test stand are significantly reduced.

Genetic Algorithms and Local Search

NASA Technical Reports Server (NTRS)

Whitley, Darrell

1996-01-01

The first part of this presentation is a tutorial level introduction to the principles of genetic search and models of simple genetic algorithms. The second half covers the combination of genetic algorithms with local search methods to produce hybrid genetic algorithms. Hybrid algorithms can be modeled within the existing theoretical framework developed for simple genetic algorithms. An application of a hybrid to geometric model matching is given. The hybrid algorithm yields results that improve on the current state-of-the-art for this problem.

WEPP FuME Analysis for a North Idaho Site

Treesearch

William Elliot; Ina Sue Miller; David Hall

2007-01-01

A computer interface has been developed to assist with analyzing soil erosion rates associated with fuel management activities. This interface uses the Water Erosion Prediction Project (WEPP) model to predict sediment yields from hillslopes and road segments to the stream network. The simple interface has a large database of climates, vegetation files and forest soil...

A case study in adaptable and reusable infrastructure at the Keck Observatory Archive: VO interfaces, moving targets, and more

NASA Astrophysics Data System (ADS)

Berriman, G. Bruce; Cohen, Richard W.; Colson, Andrew; Gelino, Christopher R.; Good, John C.; Kong, Mihseh; Laity, Anastasia C.; Mader, Jeffrey A.; Swain, Melanie A.; Tran, Hien D.; Wang, Shin-Ywan

2016-08-01

The Keck Observatory Archive (KOA) (https://koa.ipac.caltech.edu) curates all observations acquired at the W. M. Keck Observatory (WMKO) since it began operations in 1994, including data from eight active instruments and two decommissioned instruments. The archive is a collaboration between WMKO and the NASA Exoplanet Science Institute (NExScI). Since its inception in 2004, the science information system used at KOA has adopted an architectural approach that emphasizes software re-use and adaptability. This paper describes how KOA is currently leveraging and extending open source software components to develop new services and to support delivery of a complete set of instrument metadata, which will enable more sophisticated and extensive queries than currently possible. In August 2015, KOA deployed a program interface to discover public data from all instruments equipped with an imaging mode. The interface complies with version 2 of the Simple Imaging Access Protocol (SIAP), under development by the International Virtual Observatory Alliance (IVOA), which defines a standard mechanism for discovering images through spatial queries. The heart of the KOA service is an R-tree-based, database-indexing mechanism prototyped by the Virtual Astronomical Observatory (VAO) and further developed by the Montage Image Mosaic project, designed to provide fast access to large imaging data sets as a first step in creating wide-area image mosaics (such as mosaics of subsets of the 4.7 million images of the SDSS DR9 release). The KOA service uses the results of the spatial R-tree search to create an SQLite data database for further relational filtering. The service uses a JSON configuration file to describe the association between instrument parameters and the service query parameters, and to make it applicable beyond the Keck instruments. The images generated at the Keck telescope usually do not encode the image footprints as WCS fields in the FITS file headers. Because SIAP searches are spatial, much of the effort in developing the program interface involved processing the instrument and telescope parameters to understand how accurately we can derive the WCS information for each instrument. This knowledge is now being fed back into the KOA databases as part of a program to include complete metadata information for all imaging observations. The R-tree program was itself extended to support temporal (in addition to spatial) indexing, in response to requests from the planetary science community for a search engine to discover observations of Solar System objects. With this 3D-indexing scheme, the service performs very fast time and spatial matches between the target ephemerides, obtained from the JPL SPICE service. Our experiments indicate these matches can be more than 100 times faster than when separating temporal and spatial searches. Images of the tracks of the moving targets, overlaid with the image footprints, are computed with a new command-line visualization tool, mViewer, released with the Montage distribution. The service is currently in test and will be released in late summer 2016.

Simple Harmonics Motion experiment based on LabVIEW interface for Arduino

NASA Astrophysics Data System (ADS)

Tong-on, Anusorn; Saphet, Parinya; Thepnurat, Meechai

2017-09-01

In this work, we developed an affordable modern innovative physics lab apparatus. The ultrasonic sensor is used to measure the position of a mass attached on a spring as a function of time. The data acquisition system and control device were developed based on LabVIEW interface for Arduino UNO R3. The experiment was designed to explain wave propagation which is modeled by simple harmonic motion. The simple harmonic system (mass and spring) was observed and the motion can be realized using curve fitting to the wave equation in Mathematica. We found that the spring constants provided by Hooke’s law and the wave equation fit are 9.9402 and 9.1706 N/m, respectively.

Environmental Dataset Gateway (EDG) Search Widget

EPA Pesticide Factsheets

Use the Environmental Dataset Gateway (EDG) to find and access EPA's environmental resources. Many options are available for easily reusing EDG content in other other applications. This allows individuals to provide direct access to EPA's metadata outside the EDG interface. The EDG Search Widget makes it possible to search the EDG from another web page or application. The search widget can be included on your website by simply inserting one or two lines of code. Users can type a search term or lucene search query in the search field and retrieve a pop-up list of records that match that search.

EMERSE: The Electronic Medical Record Search Engine

PubMed Central

Hanauer, David A.

2006-01-01

EMERSE (The Electronic Medical Record Search Engine) is an intuitive, powerful search engine for free-text documents in the electronic medical record. It offers multiple options for creating complex search queries yet has an interface that is easy enough to be used by those with minimal computer experience. EMERSE is ideal for retrospective chart reviews and data abstraction and may have potential for clinical care as well. PMID:17238560

Standardization of search methods for guideline development: an international survey of evidence-based guideline development groups.

PubMed

Deurenberg, Rikie; Vlayen, Joan; Guillo, Sylvie; Oliver, Thomas K; Fervers, Beatrice; Burgers, Jako

2008-03-01

Effective literature searching is particularly important for clinical practice guideline development. Sophisticated searching and filtering mechanisms are needed to help ensure that all relevant research is reviewed. To assess the methods used for the selection of evidence for guideline development by evidence-based guideline development organizations. A semistructured questionnaire assessing the databases, search filters and evaluation methods used for literature retrieval was distributed to eight major organizations involved in evidence-based guideline development. All of the organizations used search filters as part of guideline development. The medline database was the primary source accessed for literature retrieval. The OVID or SilverPlatter interfaces were used in preference to the freely accessed PubMed interface. The Cochrane Library, embase, cinahl and psycinfo databases were also frequently used by the organizations. All organizations reported the intention to improve and validate their filters for finding literature specifically relevant for guidelines. In the first international survey of its kind, eight major guideline development organizations indicated a strong interest in identifying, improving and standardizing search filters to improve guideline development. It is to be hoped that this will result in the standardization of, and open access to, search filters, an improvement in literature searching outcomes and greater collaboration among guideline development organizations.

[A survey of the best bibliographic searching system in occupational medicine and discussion of its implementation].

PubMed

Inoue, J

1991-12-01

When occupational health personnel, especially occupational physicians search bibliographies, they usually have to search bibliographies by themselves. Also, if a library is not available because of the location of their work place, they might have to rely on online databases. Although there are many commercial databases in the world, people who seldom use them, will have problems with on-line searching, such as user-computer interface, keywords, and so on. The present study surveyed the best bibliographic searching system in the field of occupational medicine by questionnaire through the use of DIALOG OnDisc MEDLINE as a commercial database. In order to ascertain the problems involved in determining the best bibliographic searching system, a prototype bibliographic searching system was constructed and then evaluated. Finally, solutions for the problems were discussed. These led to the following conclusions: to construct the best bibliographic searching system at the present time, 1) a concept of micro-to-mainframe links (MML) is needed for the computer hardware network; 2) multi-lingual font standards and an excellent common user-computer interface are needed for the computer software; 3) a short course and education of database management systems, and support of personal information processing for retrieved data are necessary for the practical use of the system.

In Search of Speedier Searches.

ERIC Educational Resources Information Center

Peterson, Ivars

1984-01-01

Methods to make computer searching as simple and efficient as possible have led to the development of various data structures. Data structures specify the items involved in searching and what can be done to them. The nature and advantages of using "self-adjusting" data structures (self-adjusting binary search trees) are discussed. (JN)

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

PubMed

Smith, R F; Wiese, B A; Wojzynski, M K; Davison, D B; Worley, K C

1996-05-01

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

A Personalised Information Support System for Searching Portals and E-Resources

ERIC Educational Resources Information Center

Sirisha, B. S.; Jeevan, V. K. J.; Raja Kumar, R. V.; Goswami, A.

2009-01-01

Purpose: The purpose of this paper is to describe the development of a personalised information support system to help faculty members to search various portals and e-resources without typing the search terms in different interfaces and to obtain results re-ordered without human intervention. Design/methodology/approach: After a careful survey of…

An Improved Botanical Search Application for Middle-and High-School Students

ERIC Educational Resources Information Center

Kajiyama, Tomoko

2016-01-01

A previously reported botanical data retrieval application has been improved to make it better suited for use in middle-and high-school science classes. This search interface is ring-structured and treats multi-faceted metadata intuitively, enabling students not only to search for plant names but also to learn about the morphological features and…

Advances in Using Opensearch for Earth Science Data Discovery and Interoperability

NASA Astrophysics Data System (ADS)

Newman, D. J.; Mitchell, A. E.

2014-12-01

As per www.opensearch.org: OpenSearch is a collection of simple formats for the sharing of search results A number of organizations (NASA, ESA, CEOS) have began to adopt this standard as a means of allowing both the discovery of earth science data and the aggregation of results from disparate data archives. OpenSearch has proven to be simpler and more effective at achieving these goals than previous efforts (Catalog Service for the web for example). This talk will outline: The basic ideas behind OpenSearch The ways in which we have extended the basic specification to accomodate the Earth Science use case (two-step searching, relevancy ranking, facets) A case-study of the above in action (CWICSmart + IDN OpenSearch + CWIC OpenSearch) The potential for interoperability this simple standard affords A discussion of where we can go in the future

Transaction Logging.

ERIC Educational Resources Information Center

Jones, S.; And Others

1997-01-01

Discusses the use of transaction logging in Okapi-related projects to allow search algorithms and user interfaces to be investigated, evaluated, and compared. A series of examples is presented, illustrating logging software for character-based and graphical user interface systems, and demonstrating the usefulness of relational database management…

Wide dynamic logarithmic InGaAs sensor suitable for eye-safe active imaging

NASA Astrophysics Data System (ADS)

Ni, Yang; Bouvier, Christian; Arion, Bogdan; Noguier, Vincent

2016-05-01

In this paper, we present a simple method to analyze the injection efficiency of the photodiode interface circuit under fast shuttering conditions for active Imaging applications. This simple model has been inspired from the companion model for reactive elements largely used in CAD. In this paper, we demonstrate that traditional CTIA photodiode interface is not adequate for active imaging where fast and precise shuttering operation is necessary. Afterwards we present a direct amplification based photodiode interface which can provide an accurate and fast shuttering operation on photodiode. These considerations have been used in NIT's newly developed ROIC and corresponding SWIR sensors both in VGA 15um pitch (NSC1201) and also in QVGA 25um pitch (NSC1401).

Interfacial instability of amorphous LiPON against lithium: A combined Density Functional Theory and spectroscopic study

NASA Astrophysics Data System (ADS)

Sicolo, Sabrina; Fingerle, Mathias; Hausbrand, René; Albe, Karsten

2017-06-01

The chemical instability of the glassy solid electrolyte LiPON against metallic lithium and the occurrence of side reactions at their interface is investigated by combining a surface science approach and quantum-mechanical calculations. Using an evolutionary structure search followed by a melt-quenching protocol, a model for the disordered structure of LiPON is generated and put into contact with lithium. Even the static optimization of a simple model interface suggests that the diffusion of lithium into LiPON is driven by a considerable driving force that could easily take place under experimental conditions. Calculated reaction energies indicate that the reduction and decomposition of LiPON is thermodynamically favorable. By monitoring the evolution of the LiPON core levels as a function of lithium exposure, the disruption of the LiPON network alongside the occurrence of new phases is observed. The direct comparison between UV photoelectron spectroscopy measurements and calculated electronic densities of states for increasing stages of lithiation univocally identifies the new phases as Li2O, Li3P and Li3N. These products are stable against Li metal and form a passivation layer which shields the electrolyte from further decomposition while allowing for the diffusion of Li ions.

SunPy: Python for Solar Physics

NASA Astrophysics Data System (ADS)

Bobra, M.; Inglis, A. R.; Mumford, S.; Christe, S.; Freij, N.; Hewett, R.; Ireland, J.; Martinez Oliveros, J. C.; Reardon, K.; Savage, S. L.; Shih, A. Y.; Pérez-Suárez, D.

2017-12-01

SunPy is a community-developed open-source software library for solar physics. It is written in Python, a free, cross-platform, general-purpose, high-level programming language which is being increasingly adopted throughout the scientific community. SunPy aims to provide the software for obtaining and analyzing solar and heliospheric data. This poster introduces a new major release, SunPy version 0.8. The first major new feature introduced is Fido, the new primary interface to download data. It provides a consistent and powerful search interface to all major data providers including the VSO and the JSOC, as well as individual data sources such as GOES XRS time series. It is also easy to add new data sources as they become available, i.e. DKIST. The second major new feature is the SunPy coordinate framework. This provides a powerful way of representing coordinates, allowing simple and intuitive conversion between coordinate systems and viewpoints of different instruments (i.e., Solar Orbiter and the Parker Solar Probe), including transformation to astrophysical frames like ICRS. Other new features including new timeseries capabilities with better support for concatenation and metadata, updated documentation and example gallery. SunPy is distributed through pip and conda and all of its code is publicly available (sunpy.org).

One-to-one neuron-electrode interfacing.

PubMed

Greenbaum, Alon; Anava, Sarit; Ayali, Amir; Shein, Mark; David-Pur, Moshe; Ben-Jacob, Eshel; Hanein, Yael

2009-09-15

The question of neuronal network development and organization is a principle one, which is closely related to aspects of neuronal and network form-function interactions. In-vitro two-dimensional neuronal cultures have proved to be an attractive and successful model for the study of these questions. Research is constraint however by the search for techniques aimed at culturing stable networks, whose electrical activity can be reliably and consistently monitored. A simple approach to form small interconnected neuronal circuits while achieving one-to-one neuron-electrode interfacing is presented. Locust neurons were cultured on a novel bio-chip consisting of carbon-nanotube multi-electrode-arrays. The cells self-organized to position themselves in close proximity to the bio-chip electrodes. The organization of the cells on the electrodes was analyzed using time lapse microscopy, fluorescence imaging and scanning electron microscopy. Electrical recordings from well identified cells is presented and discussed. The unique properties of the bio-chip and the specific neuron-nanotube interactions, together with the use of relatively large insect ganglion cells, allowed long-term stabilization (as long as 10 days) of predefined neural network topology as well as high fidelity electrical recording of individual neuron firing. This novel preparation opens ample opportunity for future investigation into key neurobiological questions and principles.

Method for determining optimal supercell representation of interfaces

NASA Astrophysics Data System (ADS)

Stradi, Daniele; Jelver, Line; Smidstrup, Søren; Stokbro, Kurt

2017-05-01

The geometry and structure of an interface ultimately determines the behavior of devices at the nanoscale. We present a generic method to determine the possible lattice matches between two arbitrary surfaces and to calculate the strain of the corresponding matched interface. We apply this method to explore two relevant classes of interfaces for which accurate structural measurements of the interface are available: (i) the interface between pentacene crystals and the (1 1 1) surface of gold, and (ii) the interface between the semiconductor indium-arsenide and aluminum. For both systems, we demonstrate that the presented method predicts interface geometries in good agreement with those measured experimentally, which present nontrivial matching characteristics and would be difficult to guess without relying on automated structure-searching methods.

Evolution in the design of a low sheath-flow interface for CE-MS and application to biological samples.

PubMed

González-Ruiz, Víctor; Codesido, Santiago; Rudaz, Serge; Schappler, Julie

2018-03-01

Although several interfaces for CE-MS hyphenation are commercially available, the development of new versatile, simple and yet efficient and sensitive alternatives remains an important field of research. In a previous work, a simple low sheath-flow interface was developed from inexpensive parts. This interface features a design easy to build, maintain, and adapt to particular needs. The present work introduces an improved design of the previous interface. By reducing the diameter of the separation capillary and the emitter, a smaller Taylor cone is spontaneously formed, minimizing the zone dispersion while the analytes go through the interface and leading to less peak broadening associated to the ESI process. Numerical modeling allowed studying the mixing and diffusion processes taking place in the Taylor cone. The analytical performance of this new interface was tested with pharmaceutically relevant molecules and endogenous metabolites. The interface was eventually applied to the analysis of neural cell culture samples, allowing the identification of a panel of neurotransmission-related molecules. An excellent migration time repeatability was obtained (intra-day RSD <0.5% for most compounds, and <3.0% for inter-day precision). Most metabolites showed S/N ratios >10 with an injected volume of 6.7 nL of biological extract. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ReSEARCH: A Requirements Search Engine: Progress Report 2

DTIC Science & Technology

2008-09-01

and provides a convenient user interface for the search process. Ideally, the web application would be based on Tomcat, a free Java Servlet and JSP...Implementation issues Lucene Java is an Open Source project, available under the Apache License, which provides an accessible API for the development of...from the Apache Lucene website (Lucene- java Wiki , 2008). A search application developed with Lucene consists of the same two major com- ponents

Search Parameter Optimization for Discrete, Bayesian, and Continuous Search Algorithms

DTIC Science & Technology

2017-09-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS SEARCH PARAMETER OPTIMIZATION FOR DISCRETE , BAYESIAN, AND CONTINUOUS SEARCH ALGORITHMS by...to 09-22-2017 4. TITLE AND SUBTITLE SEARCH PARAMETER OPTIMIZATION FOR DISCRETE , BAYESIAN, AND CON- TINUOUS SEARCH ALGORITHMS 5. FUNDING NUMBERS 6...simple search and rescue acts to prosecuting aerial/surface/submersible targets on mission. This research looks at varying the known discrete and

Automatic Figure Ranking and User Interfacing for Intelligent Figure Search

PubMed Central

Yu, Hong; Liu, Feifan; Ramesh, Balaji Polepalli

2010-01-01

Background Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery. Methodology/Findings We empirically validated the hypothesis of figure ranking with over 100 bioscience researchers, and then developed unsupervised natural language processing (NLP) approaches to automatically rank figures. Evaluating on a collection of 202 full-text articles in which authors have ranked the figures based on importance, our best system achieved a weighted error rate of 0.2, which is significantly better than several other baseline systems we explored. We further explored a user interfacing application in which we built novel user interfaces (UIs) incorporating figure ranking, allowing bioscience researchers to efficiently access important figures. Our evaluation results show that 92% of the bioscience researchers prefer as the top two choices the user interfaces in which the most important figures are enlarged. With our automatic figure ranking NLP system, bioscience researchers preferred the UIs in which the most important figures were predicted by our NLP system than the UIs in which the most important figures were randomly assigned. In addition, our results show that there was no statistical difference in bioscience researchers' preference in the UIs generated by automatic figure ranking and UIs by human ranking annotation. Conclusion/Significance The evaluation results conclude that automatic figure ranking and user interfacing as we reported in this study can be fully implemented in online publishing. The novel user interface integrated with the automatic figure ranking system provides a more efficient and robust way to access scientific information in the biomedical domain, which will further enhance our existing figure search engine to better facilitate accessing figures of interest for bioscientists. PMID:20949102

Simplifying HL7 Version 3 messages.

PubMed

Worden, Robert; Scott, Philip

2011-01-01

HL7 Version 3 offers a semantically robust method for healthcare interoperability but has been criticized as overly complex to implement. This paper reviews initiatives to simplify HL7 Version 3 messaging and presents a novel approach based on semantic mapping. Based on user-defined definitions, precise transforms between simple and full messages are automatically generated. Systems can be interfaced with the simple messages and achieve interoperability with full Version 3 messages through the transforms. This reduces the costs of HL7 interfacing and will encourage better uptake of HL7 Version 3 and CDA.

Unified Desktop for Monitoring & Control Applications - The Open Navigator Framework Applied for Control Centre and EGSE Applications

NASA Astrophysics Data System (ADS)

Brauer, U.

2007-08-01

The Open Navigator Framework (ONF) was developed to provide a unified and scalable platform for user interface integration. The main objective for the framework was to raise usability of monitoring and control consoles and to provide a reuse of software components in different application areas. ONF is currently applied for the Columbus onboard crew interface, the commanding application for the Columbus Control Centre, the Columbus user facilities specialized user interfaces, the Mission Execution Crew Assistant (MECA) study and EADS Astrium internal R&D projects. ONF provides a well documented and proven middleware for GUI components (Java plugin interface, simplified concept similar to Eclipse). The overall application configuration is performed within a graphical user interface for layout and component selection. The end-user does not have to work in the underlying XML configuration files. ONF was optimized to provide harmonized user interfaces for monitoring and command consoles. It provides many convenience functions designed together with flight controllers and onboard crew: user defined workspaces, incl. support for multi screens efficient communication mechanism between the components integrated web browsing and documentation search &viewing consistent and integrated menus and shortcuts common logging and application configuration (properties) supervision interface for remote plugin GUI access (web based) A large number of operationally proven ONF components have been developed: Command Stack & History: Release of commands and follow up the command acknowledges System Message Panel: Browse, filter and search system messages/events Unified Synoptic System: Generic synoptic display system Situational Awareness : Show overall subsystem status based on monitoring of key parameters System Model Browser: Browse mission database defintions (measurements, commands, events) Flight Procedure Executor: Execute checklist and logical flow interactive procedures Web Browser : Integrated browser reference documentation and operations data Timeline Viewer: View master timeline as Gantt chart Search: Local search of operations products (e.g. documentation, procedures, displays) All GUI components access the underlying spacecraft data (commanding, reporting data, events, command history) via a common library providing adaptors for the current deployments (Columbus MCS, Columbus onboard Data Management System, Columbus Trainer raw packet protocol). New Adaptors are easy to develop. Currently an adaptor to SCOS 2000 is developed as part of a study for the ESTEC standardization section ("USS for ESTEC Reference Facility").

pyhector: A Python interface for the simple climate model Hector

DOE PAGES

Willner, Sven N.; Hartin, Corinne; Gieseke, Robert

2017-04-01

Here, pyhector is a Python interface for the simple climate model Hector (Hartin et al. 2015) developed in C++. Simple climate models like Hector can, for instance, be used in the analysis of scenarios within integrated assessment models like GCAM1, in the emulation of complex climate models, and in uncertainty analyses. Hector is an open-source, object oriented, simple global climate carbon cycle model. Its carbon cycle consists of a one pool atmosphere, three terrestrial pools which can be broken down into finer biomes or regions, and four carbon pools in the ocean component. The terrestrial carbon cycle includes primary productionmore » and respiration fluxes. The ocean carbon cycle circulates carbon via a simplified thermohaline circulation, calculating air-sea fluxes as well as the marine carbonate system. The model input is time series of greenhouse gas emissions; as example scenarios for these the Pyhector package contains the Representative Concentration Pathways (RCPs)2.« less

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

PubMed Central

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, JH Pate; Ball, Catherine A; Sherlock, Gavin

2007-01-01

Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website [1]. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat [2] on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed OntologyWidget, an easy-to-use ontology search and display tool that can be used on any web page by creating a simple html description. OntologyWidget provides a rapid auto-complete search function paired with an interactive tree display. We have developed a web service layer that communicates between the web page interface and a database of ontology terms. We currently store 40 of the ontologies from the OBO website [1], as well as a several others. These ontologies are automatically updated on a weekly basis. OntologyWidget can be used in any web-based application to take advantage of the ontologies we provide via web services or any other ontology that is provided elsewhere in the correct format. The full source code for the JavaScript and description of the OntologyWidget is available from . PMID:17854506

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

PubMed

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, J H Pate; Ball, Catherine A; Sherlock, Gavin

2007-09-13

Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat 2 on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. We have developed OntologyWidget, an easy-to-use ontology search and display tool that can be used on any web page by creating a simple html description. OntologyWidget provides a rapid auto-complete search function paired with an interactive tree display. We have developed a web service layer that communicates between the web page interface and a database of ontology terms. We currently store 40 of the ontologies from the OBO website 1, as well as a several others. These ontologies are automatically updated on a weekly basis. OntologyWidget can be used in any web-based application to take advantage of the ontologies we provide via web services or any other ontology that is provided elsewhere in the correct format. The full source code for the JavaScript and description of the OntologyWidget is available from http://smd.stanford.edu/ontologyWidget/.

Mapping of medical acronyms and initialisms to Medical Subject Headings (MeSH) across selected systems

PubMed Central

Shultz, Mary

2006-01-01

Introduction: Given the common use of acronyms and initialisms in the health sciences, searchers may be entering these abbreviated terms rather than full phrases when searching online systems. The purpose of this study is to evaluate how various MEDLINE Medical Subject Headings (MeSH) interfaces map acronyms and initialisms to the MeSH vocabulary. Methods: The interfaces used in this study were: the PubMed MeSH database, the PubMed Automatic Term Mapping feature, the NLM Gateway Term Finder, and Ovid MEDLINE. Acronyms and initialisms were randomly selected from 2 print sources. The test data set included 415 randomly selected acronyms and initialisms whose related meanings were found to be MeSH terms. Each acronym and initialism was entered into each MEDLINE MeSH interface to determine if it mapped to the corresponding MeSH term. Separately, 46 commonly used acronyms and initialisms were tested. Results: While performance differed widely, the success rates were low across all interfaces for the randomly selected terms. The common acronyms and initialisms tested at higher success rates across the interfaces, but the differences between the interfaces remained. Conclusion: Online interfaces do not always map medical acronyms and initialisms to their corresponding MeSH phrases. This may lead to inaccurate results and missed information if acronyms and initialisms are used in search strategies. PMID:17082832

Development of RESTful services and map-based user interface tools for access and delivery of data and metadata from the Marine-Geo Digital Library

NASA Astrophysics Data System (ADS)

Morton, J. J.; Ferrini, V. L.

2015-12-01

The Marine Geoscience Data System (MGDS, www.marine-geo.org) operates an interactive digital data repository and metadata catalog that provides access to a variety of marine geology and geophysical data from throughout the global oceans. Its Marine-Geo Digital Library includes common marine geophysical data types and supporting data and metadata, as well as complementary long-tail data. The Digital Library also includes community data collections and custom data portals for the GeoPRISMS, MARGINS and Ridge2000 programs, for active source reflection data (Academic Seismic Portal), and for marine data acquired by the US Antarctic Program (Antarctic and Southern Ocean Data Portal). Ensuring that these data are discoverable not only through our own interfaces but also through standards-compliant web services is critical for enabling investigators to find data of interest.Over the past two years, MGDS has developed several new RESTful web services that enable programmatic access to metadata and data holdings. These web services are compliant with the EarthCube GeoWS Building Blocks specifications and are currently used to drive our own user interfaces. New web applications have also been deployed to provide a more intuitive user experience for searching, accessing and browsing metadata and data. Our new map-based search interface combines components of the Google Maps API with our web services for dynamic searching and exploration of geospatially constrained data sets. Direct introspection of nearly all data formats for hundreds of thousands of data files curated in the Marine-Geo Digital Library has allowed for precise geographic bounds, which allow geographic searches to an extent not previously possible. All MGDS map interfaces utilize the web services of the Global Multi-Resolution Topography (GMRT) synthesis for displaying global basemap imagery and for dynamically provide depth values at the cursor location.

Connectivity algorithm with depth first search (DFS) on simple graphs

NASA Astrophysics Data System (ADS)

Riansanti, O.; Ihsan, M.; Suhaimi, D.

2018-01-01

This paper discusses an algorithm to detect connectivity of a simple graph using Depth First Search (DFS). The DFS implementation in this paper differs than other research, that is, on counting the number of visited vertices. The algorithm obtains s from the number of vertices and visits source vertex, following by its adjacent vertices until the last vertex adjacent to the previous source vertex. Any simple graph is connected if s equals 0 and disconnected if s is greater than 0. The complexity of the algorithm is O(n2).

Description of CRIB, the GIPSY retrieval mechanism, and the interface to the General Electric MARK III Service : CRIB, the mineral resources data bank of the U.S. Geological Survey--guide for public users, 1977

USGS Publications Warehouse

Calkins, James Alfred; Keefer, Eleanor K.; Ofsharick, Regina A.; Mason, George T.; Tracy, Patricia; Atkins, Mary

1978-01-01

The U.S. Geological Survey's Computerized Resources Information Bank (CRIB) is being made available for public use through the computer facilities of the University of Oklahoma and the General Electric Company, U.S.A. The use of General Electric's worldwide information-services network provides access to the CRIB file to a worldwide clientele. This manual, which consists of two chapters, is intended as a guide to users who wish to interrogate the file. Chapter A contains a description of the CRIB file, information on the use of the GIPSY retrieval system, and a description of the General Electric MARK III Service. Chapter B contains a description of the individual data items in the CRIB record as well as code lists. CRIB consists of a set of variable-length records on the metallic and nonmetallic mineral resources of the United States and other countries. At present, 31,645 records in the master file are being made available. The record contains information on mineral deposits and mineral commodities. Some topics covered are: deposit name, location, commodity information, description of deposit, geology, production, reserves, potential resources, and references. The data are processed by the GIPSY program, which maintains the data file and builds, updates, searches, and prints the records using simple yet versatile command statements. Searching and selecting records is accomplished by specifying the presence, absence, or content of any element of information in the record; these specifications can be logically linked to prepare sophisticated search strategies. Output is available in the form of the complete record, a listing of selected parts of the record, or fixed-field tabulations. The General Electric MARK III Service is a computerized information services network operating internationally by land lines, satellites, and undersea cables. The service is available by local telephone to 500 cities in North America, Western Europe, Australia, Southeast Asia, Japan, and Saudi Arabia. An interface called the 'foreground driver' is used to link the GIPSY program to the General Electric system.

A Step Beyond Simple Keyword Searches: Services Enabled by a Full Content Digital Journal Archive

NASA Technical Reports Server (NTRS)

Boccippio, Dennis J.

2003-01-01

The problems of managing and searching large archives of scientific journal articles can potentially be addressed through data mining and statistical techniques matured primarily for quantitative scientific data analysis. A journal paper could be represented by a multivariate descriptor, e.g., the occurrence counts of a number key technical terms or phrases (keywords), perhaps derived from a controlled vocabulary ( e . g . , the American Meteorological Society's Glossary of Meteorology) or bootstrapped from the journal archive itself. With this technique, conventional statistical classification tools can be leveraged to address challenges faced by both scientists and professional societies in knowledge management. For example, cluster analyses can be used to find bundles of "most-related" papers, and address the issue of journal bifurcation (when is a new journal necessary, and what topics should it encompass). Similarly, neural networks can be trained to predict the optimal journal (within a society's collection) in which a newly submitted paper should be published. Comparable techniques could enable very powerful end-user tools for journal searches, all premised on the view of a paper as a data point in a multidimensional descriptor space, e.g.: "find papers most similar to the one I am reading", "build a personalized subscription service, based on the content of the papers I am interested in, rather than preselected keywords", "find suitable reviewers, based on the content of their own published works", etc. Such services may represent the next "quantum leap" beyond the rudimentary search interfaces currently provided to end-users, as well as a compelling value-added component needed to bridge the print-to-digital-medium gap, and help stabilize professional societies' revenue stream during the print-to-digital transition.

Front-End/Gateway Software: Availability and Usefulness.

ERIC Educational Resources Information Center

Kesselman, Martin

1985-01-01

Reviews features of front-end software packages (interface between user and online system)--database selection, search strategy development, saving and downloading, hardware and software requirements, training and documentation, online systems and database accession, and costs--and discusses gateway services (user searches through intermediary…

2005 8th Annual Systems Engineering Conference. Volume 1, Tuesday

DTIC Science & Technology

2005-10-27

Services NCES Discovery Services Federated Search Denotes interface Service NCCP Oktoberfest 2004 101 Task: Global Strike Mission Planning NCCP Oktoberfest...Enterprise Service Management Security Services NCES Discovery Services Federated Search Service Test, cert and accreditation needs to be focused on small

MELTS_Excel: A Microsoft Excel-based MELTS interface for research and teaching of magma properties and evolution

NASA Astrophysics Data System (ADS)

Gualda, Guilherme A. R.; Ghiorso, Mark S.

2015-01-01

thermodynamic modeling software MELTS is a powerful tool for investigating crystallization and melting in natural magmatic systems. Rhyolite-MELTS is a recalibration of MELTS that better captures the evolution of silicic magmas in the upper crust. The current interface of rhyolite-MELTS, while flexible, can be somewhat cumbersome for the novice. We present a new interface that uses web services consumed by a VBA backend in Microsoft Excel©. The interface is contained within a macro-enabled workbook, where the user can insert the model input information and initiate computations that are executed on a central server at OFM Research. Results of simple calculations are shown immediately within the interface itself. It is also possible to combine a sequence of calculations into an evolutionary path; the user can input starting and ending temperatures and pressures, temperature and pressure steps, and the prevailing oxidation conditions. The program shows partial updates at every step of the computations; at the conclusion of the calculations, a series of data sheets and diagrams are created in a separate workbook, which can be saved independently of the interface. Additionally, the user can specify a grid of temperatures and pressures and calculate a phase diagram showing the conditions at which different phases are present. The interface can be used to apply the rhyolite-MELTS geobarometer. We demonstrate applications of the interface using an example early-erupted Bishop Tuff composition. The interface is simple to use and flexible, but it requires an internet connection. The interface is distributed for free from http://melts.ofm-research.org.

A memory-mapped output interface: Omega navigation output data from the JOLT (TM) microcomputer

NASA Technical Reports Server (NTRS)

Lilley, R. W.

1976-01-01

A hardware interface which allows both digital and analog data output from the JOLT microcomputer is described in the context of a software-based Omega Navigation receiver. The interface hardware described is designed for output of six (or eight with simple extensions) bits of binary output in response to a memory store command from the microcomputer. The interface was produced in breadboard form and is operational as an evaluation aid for the software Omega receiver.

Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

2013-12-01

The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

A simple level set method for solving Stefan problems

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

Chen, S.; Merriman, B.; Osher, S.

1997-07-15

Discussed in this paper is an implicit finite difference scheme for solving a heat equation and a simple level set method for capturing the interface between solid and liquid phases which are used to solve Stefan problems.

JSC Search System Usability Case Study

NASA Technical Reports Server (NTRS)

Meza, David; Berndt, Sarah

2014-01-01

The advanced nature of "search" has facilitated the movement from keyword match to the delivery of every conceivable information topic from career, commerce, entertainment, learning... the list is infinite. At NASA Johnson Space Center (JSC ) the Search interface is an important means of knowledge transfer. By indexing multiple sources between directorates and organizations, the system's potential is culture changing in that through search, knowledge of the unique accomplishments in engineering and science can be seamlessly passed between generations. This paper reports the findings of an initial survey, the first of a four part study to help determine user sentiment on the intranet, or local (JSC) enterprise search environment as well as the larger NASA enterprise. The survey is a means through which end users provide direction on the development and transfer of knowledge by way of the search experience. The ideal is to identify what is working and what needs to be improved from the users' vantage point by documenting: (1) Where users are satisfied/dissatisfied (2) Perceived value of interface components (3) Gaps which cause any disappointment in search experience. The near term goal is it to inform JSC search in order to improve users' ability to utilize existing services and infrastructure to perform tasks with a shortened life cycle. Continuing steps include an agency based focus with modified questions to accomplish a similar purpose

SPIRE: Systematic protein investigative research environment.

PubMed

Kolker, Eugene; Higdon, Roger; Morgan, Phil; Sedensky, Margaret; Welch, Dean; Bauman, Andrew; Stewart, Elizabeth; Haynes, Winston; Broomall, William; Kolker, Natali

2011-12-10

The SPIRE (Systematic Protein Investigative Research Environment) provides web-based experiment-specific mass spectrometry (MS) proteomics analysis (https://www.proteinspire.org). Its emphasis is on usability and integration of the best analytic tools. SPIRE provides an easy to use web-interface and generates results in both interactive and simple data formats. In contrast to run-based approaches, SPIRE conducts the analysis based on the experimental design. It employs novel methods to generate false discovery rates and local false discovery rates (FDR, LFDR) and integrates the best and complementary open-source search and data analysis methods. The SPIRE approach of integrating X!Tandem, OMSSA and SpectraST can produce an increase in protein IDs (52-88%) over current combinations of scoring and single search engines while also providing accurate multi-faceted error estimation. One of SPIRE's primary assets is combining the results with data on protein function, pathways and protein expression from model organisms. We demonstrate some of SPIRE's capabilities by analyzing mitochondrial proteins from the wild type and 3 mutants of C. elegans. SPIRE also connects results to publically available proteomics data through its Model Organism Protein Expression Database (MOPED). SPIRE can also provide analysis and annotation for user supplied protein ID and expression data. Copyright © 2011. Published by Elsevier B.V.

The Simple Concurrent Online Processing System (SCOPS) - An open-source interface for remotely sensed data processing

NASA Astrophysics Data System (ADS)

Warren, M. A.; Goult, S.; Clewley, D.

2018-06-01

Advances in technology allow remotely sensed data to be acquired with increasingly higher spatial and spectral resolutions. These data may then be used to influence government decision making and solve a number of research and application driven questions. However, such large volumes of data can be difficult to handle on a single personal computer or on older machines with slower components. Often the software required to process data is varied and can be highly technical and too advanced for the novice user to fully understand. This paper describes an open-source tool, the Simple Concurrent Online Processing System (SCOPS), which forms part of an airborne hyperspectral data processing chain that allows users accessing the tool over a web interface to submit jobs and process data remotely. It is demonstrated using Natural Environment Research Council Airborne Research Facility (NERC-ARF) instruments together with other free- and open-source tools to take radiometrically corrected data from sensor geometry into geocorrected form and to generate simple or complex band ratio products. The final processed data products are acquired via an HTTP download. SCOPS can cut data processing times and introduce complex processing software to novice users by distributing jobs across a network using a simple to use web interface.

Strategic Help in User Interfaces for Information Retrieval.

ERIC Educational Resources Information Center

Brajnik, Giorgio; Mizzaro, Stefano; Tasso, Carlo; Venuti, Fabio

2002-01-01

Discussion of search strategy in information retrieval by end users focuses on the role played by strategic reasoning and design principles for user interfaces. Highlights include strategic help based on collaborative coaching; a conceptual model for strategic help; and a prototype knowledge-based system named FIRE. (Author/LRW)

OASIS: Prototyping Graphical Interfaces to Networked Information.

ERIC Educational Resources Information Center

Buckland, Michael K.; And Others

1993-01-01

Describes the latest modifications being made to OASIS, a front-end enhancement to the University of California's MELVYL online union catalog. Highlights include the X Windows interface; multiple database searching to act as an information network; Lisp implementation for flexible data representation; and OASIS commands and features to help…

A User Interface for Multiple Retrieval Systems.

ERIC Educational Resources Information Center

Teskey, Niall; And Others

1987-01-01

Reviews current systems designed to help end-users search online databases without the assistance of an intermediary and describes a prototype system which emulates the Deco (the text storage and retrieval system used by Unilever) interface on Dialog and Data-Star. Initial trials of the prototype system are reported. (15 references) (MES)

The Impact of Text Browsing on Text Retrieval Performance.

ERIC Educational Resources Information Center

Bodner, Richard C.; Chignell, Mark H.; Charoenkitkarn, Nipon; Golovchinsky, Gene; Kopak, Richard W.

2001-01-01

Compares empirical results from three experiments using Text Retrieval Conference (TREC) data and search topics that involved three different user interfaces. Results show that marking Boolean queries on text, which encourages browsing, and hypertext interfaces to text retrieval systems can benefit recall and can also benefit novice users.…

Web OPAC Interfaces: An Overview.

ERIC Educational Resources Information Center

Babu, B. Ramesh; O'Brien, Ann

2000-01-01

Discussion of Web-based online public access catalogs (OPACs) focuses on a review of six Web OPAC interfaces in use in academic libraries in the United Kingdom. Presents a checklist and guidelines of important features and functions that are currently available, including search strategies, access points, display, links, and layout. (Author/LRW)

LISA's Move from SilverPlatter to Bowker--Looking at the Interface.

ERIC Educational Resources Information Center

Stein, Jonathan

1994-01-01

Compares LISA (Library and Information Science Abstracts) on SilverPlatter's CD-ROM with its replacement version, Bowker-Saur's LISA Plus. Features reviewed include entry to the databases; use of Boolean search facilities; indexes and browsing; displaying and printing records; subsidiary functions; on-screen help; and interfaces. (Contains eight…

SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

PubMed

Lekschas, Fritz; Gehlenborg, Nils

2018-04-01

The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest. We developed SATORI-an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection. SATORI enables researchers to seamlessly search, browse and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface. SATORI is an open-source web application, which is freely available at http://satori.refinery-platform.org and integrated into the Refinery Platform. nils@hms.harvard.edu. Supplementary data are available at Bioinformatics online.

Theoretical Analysis of Local Search and Simple Evolutionary Algorithms for the Generalized Travelling Salesperson Problem.

PubMed

Pourhassan, Mojgan; Neumann, Frank

2018-06-22

The generalized travelling salesperson problem is an important NP-hard combinatorial optimization problem for which meta-heuristics, such as local search and evolutionary algorithms, have been used very successfully. Two hierarchical approaches with different neighbourhood structures, namely a Cluster-Based approach and a Node-Based approach, have been proposed by Hu and Raidl (2008) for solving this problem. In this paper, local search algorithms and simple evolutionary algorithms based on these approaches are investigated from a theoretical perspective. For local search algorithms, we point out the complementary abilities of the two approaches by presenting instances where they mutually outperform each other. Afterwards, we introduce an instance which is hard for both approaches when initialized on a particular point of the search space, but where a variable neighbourhood search combining them finds the optimal solution in polynomial time. Then we turn our attention to analysing the behaviour of simple evolutionary algorithms that use these approaches. We show that the Node-Based approach solves the hard instance of the Cluster-Based approach presented in Corus et al. (2016) in polynomial time. Furthermore, we prove an exponential lower bound on the optimization time of the Node-Based approach for a class of Euclidean instances.

Quality of anaesthesia-related information accessed via Internet searches.

PubMed

Caron, S; Berton, J; Beydon, L

2007-08-01

We conducted a study to examine the quality and stability of information available from the Internet on four anaesthesia-related topics. In January 2006, we searched using four key words (porphyria, scleroderma, transfusion risk, and epidural analgesia risk) with five search engines (Google, HotBot, AltaVista, Excite, and Yahoo). We used a published scoring system (NetScoring) to evaluate the first 15 sites identified by each of these 20 searches. We also used a simple four-point scale to assess the first 100 sites in the Google search on one of our four topics ('epidural analgesia risk'). In November 2006, we conducted a second evaluation, using three search engines (Google, AltaVista, and Yahoo) with 14 synonyms for 'epidural analgesia risk'. The five search engines performed similarly. NetScoring scores were lower for transfusion risk (P < 0.001). One or more high-quality sites was identified consistently among the first 15 sites in each search. Quality scored using the simple scale correlated closely with medical content and design by NetScoring and with the number of references (P < 0.05). Synonyms of 'epidural analgesia risk' yielded similar results. The quality of accessed information improved somewhat over the 11 month period with Yahoo and AltaVista, but declined with Google. The Internet is a valuable tool for obtaining medical information, but the quality of websites varies between different topics. A simple rating scale may facilitate the quality scoring on individual websites. Differences in precise search terms used for a given topic did not appear to affect the quality of the information obtained.

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database.

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful AOP-DB user interface in...

User's manual for interfacing a leading edge, vortex rollup program with two linear panel methods

NASA Technical Reports Server (NTRS)

Desilva, B. M. E.; Medan, R. T.

1979-01-01

Sufficient instructions are provided for interfacing the Mangler-Smith, leading edge vortex rollup program with a vortex lattice (POTFAN) method and an advanced higher order, singularity linear analysis for computing the vortex effects for simple canard wing combinations.

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful user interface in the for...

Innovative Science Experiments Using Phoenix

ERIC Educational Resources Information Center

Kumar, B. P. Ajith; Satyanarayana, V. V. V.; Singh, Kundan; Singh, Parmanand

2009-01-01

A simple, flexible and very low cost hardware plus software framework for developing computer-interfaced science experiments is presented. It can be used for developing computer-interfaced science experiments without getting into the details of electronics or computer programming. For developing experiments this is a middle path between…

Experimental research control software system

NASA Astrophysics Data System (ADS)

Cohn, I. A.; Kovalenko, A. G.; Vystavkin, A. N.

2014-05-01

A software system, intended for automation of a small scale research, has been developed. The software allows one to control equipment, acquire and process data by means of simple scripts. The main purpose of that development is to increase experiment automation easiness, thus significantly reducing experimental setup automation efforts. In particular, minimal programming skills are required and supervisors have no reviewing troubles. Interactions between scripts and equipment are managed automatically, thus allowing to run multiple scripts simultaneously. Unlike well-known data acquisition commercial software systems, the control is performed by an imperative scripting language. This approach eases complex control and data acquisition algorithms implementation. A modular interface library performs interaction with external interfaces. While most widely used interfaces are already implemented, a simple framework is developed for fast implementations of new software and hardware interfaces. While the software is in continuous development with new features being implemented, it is already used in our laboratory for automation of a helium-3 cryostat control and data acquisition. The software is open source and distributed under Gnu Public License.

Technologies and practices for maintaining and publishing earth science vocabularies

NASA Astrophysics Data System (ADS)

Cox, Simon; Yu, Jonathan; Williams, Megan; Giabardo, Fabrizio; Lowe, Dominic

2015-04-01

Shared vocabularies are a key element in geoscience data interoperability. Many organizations curate vocabularies, with most Geologic Surveys having a long history of development of lexicons and authority tables. However, their mode of publication is heterogeneous, ranging from PDFs and HTML web pages, spreadsheets and CSV, through various user-interfaces, and public and private APIs. Content maintenance ranges from tightly-governed and externally opaque, through various community processes, all the way to crowd-sourcing ('folksonomies'). Meanwhile, there is an increasing expectation of greater harmonization and vocabulary re-use, which create requirements for standardized content formalization and APIs, along with transparent content maintenance and versioning. We have been trialling a combination of processes and software dealing with vocabulary formalization, registration, search and linking. We use the Simplified Knowledge Organization System (SKOS) to provide a generic interface to content. SKOS is an RDF technology for multi-lingual, hierarchical vocabularies, oriented around 'concepts' denoted by URIs, and thus consistent with Linked Open Data. SKOS may be mixed in with classes and properties from specialized ontologies which provide a more specific interface when required. We have developed a suite of practices and techniques for conversion of content from the source technologies and styles into SKOS, largely based on spreadsheet manipulation before RDF conversion, and SPARQL afterwards. The workflow for each vocabulary must be adapted to match the specific inputs. In linked data applications, two requirements are paramount for user confidence: (i) the URI that denotes a vocabulary item is persistent, and should be dereferenceable indefinitely; (ii) the history and status of the resource denoted by a URI must be available. This is implemented by the Linked Data Registry (LDR), originally developed for the World Meteorological Organization and the UK Environment Agency, and now adapted and enhanced for deployment by CSIRO and the Australian Bureau of Meteorology. The LDR applies a standard content registration paradigm to RDF data, also including a delegation mode that enables a system to register (endorse) externally managed content. The locally managed RDF is exposed on a SPARQL endpoint. The registry implementation enables a flexible interaction pattern to support various specific content publication workflows, with the key feature of making the content externally accessible through a standard interface alongside its history, previous versions, and status. SPARQL is the standard low-level API for RDF including SKOS. On top of this we have developed SISSvoc, a SKOS-based RESTful API. This has been used it to deploy a number of vocabularies on behalf of the IUGS, ICS, NERC, OGC, the Australian Government, and CSIRO projects. Applications like SISSvoc Search provide a simple search UI on top of one or more SISSvoc sources. Together, these components provide a powerful and flexible system for providing earth science vocabularies for the community, consistent with semantic web and linked-data principles.

New Capabilities in the Astrophysics Multispectral Archive Search Engine

NASA Astrophysics Data System (ADS)

Cheung, C. Y.; Kelley, S.; Roussopoulos, N.

The Astrophysics Multispectral Archive Search Engine (AMASE) uses object-oriented database techniques to provide a uniform multi-mission and multi-spectral interface to search for data in the distributed archives. We describe our experience of porting AMASE from Illustra object-relational DBMS to the Informix Universal Data Server. New capabilities and utilities have been developed, including a spatial datablade that supports Nearest Neighbor queries.

FOUNTAIN: A JAVA open-source package to assist large sequencing projects

PubMed Central

Buerstedde, Jean-Marie; Prill, Florian

2001-01-01

Background Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences. Results We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented. Conclusions A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort. PMID:11591214

Searching social networks for subgraph patterns

NASA Astrophysics Data System (ADS)

Ogaard, Kirk; Kase, Sue; Roy, Heather; Nagi, Rakesh; Sambhoos, Kedar; Sudit, Moises

2013-06-01

Software tools for Social Network Analysis (SNA) are being developed which support various types of analysis of social networks extracted from social media websites (e.g., Twitter). Once extracted and stored in a database such social networks are amenable to analysis by SNA software. This data analysis often involves searching for occurrences of various subgraph patterns (i.e., graphical representations of entities and relationships). The authors have developed the Graph Matching Toolkit (GMT) which provides an intuitive Graphical User Interface (GUI) for a heuristic graph matching algorithm called the Truncated Search Tree (TruST) algorithm. GMT is a visual interface for graph matching algorithms processing large social networks. GMT enables an analyst to draw a subgraph pattern by using a mouse to select categories and labels for nodes and links from drop-down menus. GMT then executes the TruST algorithm to find the top five occurrences of the subgraph pattern within the social network stored in the database. GMT was tested using a simulated counter-insurgency dataset consisting of cellular phone communications within a populated area of operations in Iraq. The results indicated GMT (when executing the TruST graph matching algorithm) is a time-efficient approach to searching large social networks. GMT's visual interface to a graph matching algorithm enables intelligence analysts to quickly analyze and summarize the large amounts of data necessary to produce actionable intelligence.

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

PubMed

Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

2007-07-01

We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

Structure and functions of water-membrane interfaces and their role in proto-biological evolution

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M.; Macelroy, R. D.

1991-01-01

Among the most important developments in proto-biological evolution was the emergence of membrane-like structures. These are formed by spontaneous association of relatively simple amphiphilic molecules that would have been readily available in the primordial environment. The resulting interfacial regions between water and nonpolar interior of the membrane have several properties which made them uniquely suitable for promoting subsequent evolution. They can (1) selectively attract organic material and mediate its transport, (2) serve as simple catalysts for chemical reactions, and (3) promote the formation of trans-membrane electrical and chemical gradients which could provide energy sources for proto-cells. Understanding the structure of interfaces, their interactions with organic molecules and molecular mechanisms of their functions is an essential step to understanding proto-biological evolution. In our computer simulation studies, we showed that the structure of water at interfaces with nonpolar media is significantly different from that in the bulk. In particular, the average surface dipole density points from the vapor to the liquid. As a result, negative ions can approach the interface more easily than positive ions. Amphiphilic molecules composed of hydrocarbon conjugated rings and polar substituents (e.g., phenol) assume at the interface rigid orientations in which polar groups are buried in water while hydrocarbon parts are located in the nonpolar environment. These orientational differences are of special interest in connection with the ability of some of these molecules to efficiently absorb photons. Flexible molecules with polar substituents often adopt at interfaces conformations different from those in the bulk aquaeous solution and in the gas phase. As a result, in many instances both specificity and kinetics of chemical reactions in which these molecules can participate is modified by the presence of surfaces. Of special interest is the mechanism by which polar molecules are transferred across interface between water and a nonpolar medium. Our recent study showed that simple ionophores bind ions by the same mechanisms as ion channels and carriers from modern cells.

Some thoughts on the management of large, complex international space ventures

NASA Technical Reports Server (NTRS)

Lee, T. J.; Kutzer, Ants; Schneider, W. C.

1992-01-01

Management issues relevant to the development and deployment of large international space ventures are discussed with particular attention given to previous experience. Management approaches utilized in the past are labeled as either simple or complex, and signs of efficient management are examined. Simple approaches include those in which experiments and subsystems are developed for integration into spacecraft, and the Apollo-Soyuz Test Project is given as an example of a simple multinational approach. Complex approaches include those for ESA's Spacelab Project and the Space Station Freedom in which functional interfaces cross agency and political boundaries. It is concluded that individual elements of space programs should be managed by individual participating agencies, and overall configuration control is coordinated by level with a program director acting to manage overall objectives and project interfaces.

A Framework for Integrating Oceanographic Data Repositories

NASA Astrophysics Data System (ADS)

Rozell, E.; Maffei, A. R.; Beaulieu, S. E.; Fox, P. A.

2010-12-01

Oceanographic research covers a broad range of science domains and requires a tremendous amount of cross-disciplinary collaboration. Advances in cyberinfrastructure are making it easier to share data across disciplines through the use of web services and community vocabularies. Best practices in the design of web services and vocabularies to support interoperability amongst science data repositories are only starting to emerge. Strategic design decisions in these areas are crucial to the creation of end-user data and application integration tools. We present S2S, a novel framework for deploying customizable user interfaces to support the search and analysis of data from multiple repositories. Our research methods follow the Semantic Web methodology and technology development process developed by Fox et al. This methodology stresses the importance of close scientist-technologist interactions when developing scientific use cases, keeping the project well scoped and ensuring the result meets a real scientific need. The S2S framework motivates the development of standardized web services with well-described parameters, as well as the integration of existing web services and applications in the search and analysis of data. S2S also encourages the use and development of community vocabularies and ontologies to support federated search and reduce the amount of domain expertise required in the data discovery process. S2S utilizes the Web Ontology Language (OWL) to describe the components of the framework, including web service parameters, and OpenSearch as a standard description for web services, particularly search services for oceanographic data repositories. We have created search services for an oceanographic metadata database, a large set of quality-controlled ocean profile measurements, and a biogeographic search service. S2S provides an application programming interface (API) that can be used to generate custom user interfaces, supporting data and application integration across these repositories and other web resources. Although initially targeted towards a general oceanographic audience, the S2S framework shows promise in many science domains, inspired in part by the broad disciplinary coverage of oceanography. This presentation will cover the challenges addressed by the S2S framework, the research methods used in its development, and the resulting architecture for the system. It will demonstrate how S2S is remarkably extensible, and can be generalized to many science domains. Given these characteristics, the framework can simplify the process of data discovery and analysis for the end user, and can help to shift the responsibility of search interface development away from data managers.

Emergence of an optimal search strategy from a simple random walk

PubMed Central

Sakiyama, Tomoko; Gunji, Yukio-Pegio

2013-01-01

In reports addressing animal foraging strategies, it has been stated that Lévy-like algorithms represent an optimal search strategy in an unknown environment, because of their super-diffusion properties and power-law-distributed step lengths. Here, starting with a simple random walk algorithm, which offers the agent a randomly determined direction at each time step with a fixed move length, we investigated how flexible exploration is achieved if an agent alters its randomly determined next step forward and the rule that controls its random movement based on its own directional moving experiences. We showed that our algorithm led to an effective food-searching performance compared with a simple random walk algorithm and exhibited super-diffusion properties, despite the uniform step lengths. Moreover, our algorithm exhibited a power-law distribution independent of uniform step lengths. PMID:23804445

Emergence of an optimal search strategy from a simple random walk.

PubMed

Sakiyama, Tomoko; Gunji, Yukio-Pegio

2013-09-06

In reports addressing animal foraging strategies, it has been stated that Lévy-like algorithms represent an optimal search strategy in an unknown environment, because of their super-diffusion properties and power-law-distributed step lengths. Here, starting with a simple random walk algorithm, which offers the agent a randomly determined direction at each time step with a fixed move length, we investigated how flexible exploration is achieved if an agent alters its randomly determined next step forward and the rule that controls its random movement based on its own directional moving experiences. We showed that our algorithm led to an effective food-searching performance compared with a simple random walk algorithm and exhibited super-diffusion properties, despite the uniform step lengths. Moreover, our algorithm exhibited a power-law distribution independent of uniform step lengths.

Exploring Google to Enhance Reference Services

ERIC Educational Resources Information Center

Jia, Peijun

2011-01-01

Google is currently recognized as the world's most powerful search engine. Google is so powerful and intuitive that one does not need to possess many skills to use it. However, Google is more than just simple search. For those who have special search skills and know Google's superior search features, it becomes an extraordinary tool. To understand…

Millennial Students' Mental Models of Search: Implications for Academic Librarians and Database Developers

ERIC Educational Resources Information Center

Holman, Lucy

2011-01-01

Today's students exhibit generational differences in the way they search for information. Observations of first-year students revealed a proclivity for simple keyword or phrases searches with frequent misspellings and incorrect logic. Although no students had strong mental models of search mechanisms, those with stronger models did construct more…

Multiplexing of adjacent vortex modes with the forked grating coupler

NASA Astrophysics Data System (ADS)

Nadovich, Christopher T.; Kosciolek, Derek J.; Crouse, David T.; Jemison, William D.

2017-08-01

For vortex fiber multiplexing to reach practical commercial viability, simple silicon photonic interfaces with vortex fiber will be required. These interfaces must support multiplexing. Toward this goal, an efficient singlefed multimode Forked Grating Coupler (FGC) for coupling two different optical vortex OAM charges to or from the TE0 and TE1 rectangular waveguide modes has been developed. A simple, apodized device implemented with e-beam lithography and a conventional dual-etch processing on SOI wafer exhibits low crosstalk and reasonable mode match. Advanced designs using this concept are expected to further improve performance.

Effective Use of SMSS: A Simple Strategy and Sample Implementation

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

Hensinger, David

1998-09-30

The purpose of this document is to present a strategy for effectively using SMSS (Sea.leable Mass Storage System) and to distribute a simple implementation of this strategy. This work was done as a stopgap memure to ~lOW ~ ~~yst to USe the storage Power of SMSS in the absence of a more user friendly interface. The features and functionality discussed in this document represent a minimum set of capabilities to allow a useful archiving interface functionality. The implementation presented is the most basic possible and would benefit significantly from an organized support and documentation effort.

The Information System at CeSAM

NASA Astrophysics Data System (ADS)

Agneray, F.; Gimenez, S.; Moreau, C.; Roehlly, Y.

2012-09-01

Modern large observational programmes produce important amounts of data from various origins, and need high level quality control, fast data access via easy-to-use graphic interfaces, as well as possibility to cross-correlate informations coming from different observations. The Centre de donnéeS Astrophysique de Marseille (CeSAM) offer web access to VO compliant Information Systems to access data of different projects (VVDS, HeDAM, EXODAT, HST-COSMOS,…), including ancillary data obtained outside Laboratoire d'Astrophysique de Marseille (LAM) control. The CeSAM Information Systems provides download of catalogues and some additional services like: search, extract and display imaging and spectroscopic data by multi-criteria and Cone Search interfaces.

RoboCup-Rescue: an international cooperative research project of robotics and AI for the disaster mitigation problem

NASA Astrophysics Data System (ADS)

Tadokoro, Satoshi; Kitano, Hiroaki; Takahashi, Tomoichi; Noda, Itsuki; Matsubara, Hitoshi; Shinjoh, Atsushi; Koto, Tetsuo; Takeuchi, Ikuo; Takahashi, Hironao; Matsuno, Fumitoshi; Hatayama, Mitsunori; Nobe, Jun; Shimada, Susumu

2000-07-01

This paper introduces the RoboCup-Rescue Simulation Project, a contribution to the disaster mitigation, search and rescue problem. A comprehensive urban disaster simulator is constructed on distributed computers. Heterogeneous intelligent agents such as fire fighters, victims and volunteers conduct search and rescue activities in this virtual disaster world. A real world interface integrates various sensor systems and controllers of infrastructures in the real cities with the real world. Real-time simulation is synchronized with actual disasters, computing complex relationship between various damage factors and agent behaviors. A mission-critical man-machine interface provides portability and robustness of disaster mitigation centers, and augmented-reality interfaces for rescue in real disasters. It also provides a virtual- reality training function for the public. This diverse spectrum of RoboCup-Rescue contributes to the creation of the safer social system.

Standardized mappings--a framework to combine different semantic mappers into a standardized web-API.

PubMed

Neuhaus, Philipp; Doods, Justin; Dugas, Martin

2015-01-01

Automatic coding of medical terms is an important, but highly complicated and laborious task. To compare and evaluate different strategies a framework with a standardized web-interface was created. Two UMLS mapping strategies are compared to demonstrate the interface. The framework is a Java Spring application running on a Tomcat application server. It accepts different parameters and returns results in JSON format. To demonstrate the framework, a list of medical data items was mapped by two different methods: similarity search in a large table of terminology codes versus search in a manually curated repository. These mappings were reviewed by a specialist. The evaluation shows that the framework is flexible (due to standardized interfaces like HTTP and JSON), performant and reliable. Accuracy of automatically assigned codes is limited (up to 40%). Combining different semantic mappers into a standardized Web-API is feasible. This framework can be easily enhanced due to its modular design.

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

Interface Design Concepts in the Development of ELSA, an Intelligent Electronic Library Search Assistant.

ERIC Educational Resources Information Center

Denning, Rebecca; Smith, Philip J.

1994-01-01

Describes issues and advances in the design of appropriate inference engines and knowledge structures needed by commercially feasible intelligent intermediary systems for information retrieval. Issues associated with the design of interfaces to such functions are discussed in detail. Design principles for guiding implementation of these interfaces…

Searching on the Run

ERIC Educational Resources Information Center

Tenopir, Carol

2004-01-01

With wireless connectivity and small laptop computers, people are no longer tied to the desktop for online searching. Handheld personal digital assistants (PDAs) offer even greater portability. So far, the most common uses of PDAs are as calendars and address books, or to interface with a laptop or desktop machine. More advanced PDAs, like…

Monte Carlo-based searching as a tool to study carbohydrate structure

USDA-ARS?s Scientific Manuscript database

A torsion angle-based Monte-Carlo searching routine was developed and applied to several carbohydrate modeling problems. The routine was developed as a Unix shell script that calls several programs, which allows it to be interfaced with multiple potential functions and various functions for evaluat...

Mechanisms of Surface-Mediated DNA Hybridization

PubMed Central

2015-01-01

Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100 000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state. PMID:24708278

A CLIPS-based tool for aircraft pilot-vehicle interface design

NASA Technical Reports Server (NTRS)

Fowler, Thomas D.; Rogers, Steven P.

1991-01-01

The Pilot-Vehicle Interface of modern aircraft is the cognitive, sensory, and psychomotor link between the pilot, the avionics modules, and all other systems on board the aircraft. To assist pilot-vehicle interface designers, a C Language Integrated Production System (CLIPS) based tool was developed that allows design information to be stored in a table that can be modified by rules representing design knowledge. Developed for the Apple Macintosh, the tool allows users without any CLIPS programming experience to form simple rules using a point and click interface.

Supporting Flight Control for UAV-Assisted Wilderness Search and Rescue Through Human Centered Interface Design

DTIC Science & Technology

2007-12-01

have found that increased realism typically makes a more impressive looking interface, but not always a more effective interface [53]. Some display...intended positions. Other, more cinematic meth- ods may look more impressive, but looking better is not necessarily more effective at supporting... realism : Misplaced faith in realis- tic displays. Ergonomics in Design: Magazine of Human Factors Applications, 13(3):6–13, 2005. [54] H. S. Smallman, M. St

DRUMS: a human disease related unique gene mutation search engine.

PubMed

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

A Land-Use-Planning Simulation Using Google Earth

ERIC Educational Resources Information Center

Bodzin, Alec M.; Cirucci, Lori

2009-01-01

Google Earth (GE) is proving to be a valuable tool in the science classroom for understanding the environment and making responsible environmental decisions (Bodzin 2008). GE provides learners with a dynamic mapping experience using a simple interface with a limited range of functions. This interface makes geospatial analysis accessible and…

Lab Inputs for Common Micros.

ERIC Educational Resources Information Center

Tinker, Robert

1984-01-01

The game paddle inputs of Apple microcomputers provide a simple way to get laboratory measurements into the computer. Discusses these game paddles and the necessary interface software. Includes schematics for Apple built-in paddle electronics, TRS-80 game paddle I/O, Commodore circuit for user port, and bus interface for Sinclair/Timex, Commodore,…

New Features in ADS Labs

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto; Kurtz, M. J.; Henneken, E. A.; Grant, C. S.; Thompson, D.; Di Milia, G.; Luker, J.; Murray, S. S.

2013-01-01

The NASA Astrophysics Data System (ADS) has been working hard on updating its services and interfaces to better support our community's research needs. ADS Labs is a new interface built on the old tried-and-true ADS Abstract Databases, so all of ADS's content is available through it. In this presentation we highlight the new features that have been developed in ADS Labs over the last year: new recommendations, metrics, a citation tool and enhanced fulltext search. ADS Labs has long been providing article-level recommendations based on keyword similarity, co-readership and co-citation analysis of its corpus. We have now introduced personal recommendations, which provide a list of articles to be considered based on a individual user's readership history. A new metrics interface provides a summary of the basic impact indicators for a list of records. These include the total and normalized number of papers, citations, reads, and downloads. Also included are some of the popular indices such as the h, g and i10 index. The citation helper tool allows one to submit a set of records and obtain a list of top 10 papers which cite and/or are cited by papers in the original list (but which are not in it). The process closely resembles the network approach of establishing "friends of friends" via an analysis of the citation network. The full-text search service now covers more than 2.5 million documents, including all the major astronomy journals, as well as physics journals published by Springer, Elsevier, the American Physical Society, the American Geophysical Union, and all of the arXiv eprints. The full-text search interface interface allows users and librarians to dig deep and find words or phrases in the body of the indexed articles. ADS Labs is available at http://adslabs.org

Microleakage at the Different Implant Abutment Interface: A Systematic Review

PubMed Central

Chowdhary, Ramesh; Kumari, Shail

2017-01-01

Introduction Presence of gap at the implant-abutment interface, leads to microleakage and accumulation of bacteria which can affect the success of dental implants. Aim To evaluate the sealing capability of different implant connections against microleakage. Materials and Methods In January 2017 an electronic search of literature was performed, in Medline, EBSCO host and Pubmed data base. The search was focused on ability of different implant connections in preventing microleakage. The related titles and abstracts available in English were screened, and the articles that fulfilled the inclusion criteria were selected for full text reading. Results In this systematic review, literature search initially resulted in 78 articles among which 30 articles only fulfilled the criteria for inclusion and were finally included in the review. Almost all the studies showed that there was some amount of microleakage at abutment implant interface. Microleakage was very less in Morse taper implants in comparison to other implant connections. Majority of studies showed less microleakage in static loading conditions and microleakage increases in dynamic loading conditions. Conclusion In this systematic review maximum studies showed that there was some amount of microleakage at abutment implant interface. External hexagon implants failed completely to prevent microleakage in both static and dynamic loading conditions of implants. Internal hexagon implants mainly internal conical (Morse taper) implants are very promising in case of static loading and also showed less microleakage in dynamic loading conditions. Torque recommended by manufacturer should be followed strictly to get a better seal at abutment implant interface. Zirconia abutments are more to microleakage than Titanium abutments and there use should be discouraged. Zirconia abutments should be only restricted to cases where there was very high demand of aesthetics. PMID:28764310

Improving Web Searches: Case Study of Quit-Smoking Web Sites for Teenagers

PubMed Central

Skinner, Harvey

2003-01-01

Background The Web has become an important and influential source of health information. With the vast number of Web sites on the Internet, users often resort to popular search sites when searching for information. However, little is known about the characteristics of Web sites returned by simple Web searches for information about smoking cessation for teenagers. Objective To determine the characteristics of Web sites retrieved by search engines about smoking cessation for teenagers and how information quality correlates with the search ranking. Methods The top 30 sites returned by 4 popular search sites in response to the search terms "teen quit smoking" were examined. The information relevance and quality characteristics of these sites were evaluated by 2 raters. Objective site characteristics were obtained using a page-analysis Web site. Results Only 14 of the 30 Web sites are of direct relevance to smoking cessation for teenagers. The readability of about two-thirds of the 14 sites is below an eighth-grade school level and they ranked significantly higher (Kendall rank correlation, tau = -0.39, P= .05) in search-site results than sites with readability above or equal to that grade level. Sites that ranked higher were significantly associated with the presence of e-mail address for contact (tau = -0.46, P= .01), annotated hyperlinks to external sites (tau = -0.39, P= .04), and the presence of meta description tag (tau = -0.48, P= .002). The median link density (number of external sites that have a link to that site) of the Web pages was 6 and the maximum was 735. A higher link density was significantly associated with a higher rank (tau = -0.58, P= .02). Conclusions Using simple search terms on popular search sites to look for information on smoking cessation for teenagers resulted in less than half of the sites being of direct relevance. To improve search efficiency, users could supplement results obtained from simple Web searches with human-maintained Web directories and learn to refine their searches with more advanced search syntax. PMID:14713656

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

A modeling paradigm for interdisciplinary water resources modeling: Simple Script Wrappers (SSW)

NASA Astrophysics Data System (ADS)

Steward, David R.; Bulatewicz, Tom; Aistrup, Joseph A.; Andresen, Daniel; Bernard, Eric A.; Kulcsar, Laszlo; Peterson, Jeffrey M.; Staggenborg, Scott A.; Welch, Stephen M.

2014-05-01

Holistic understanding of a water resources system requires tools capable of model integration. This team has developed an adaptation of the OpenMI (Open Modelling Interface) that allows easy interactions across the data passed between models. Capabilities have been developed to allow programs written in common languages such as matlab, python and scilab to share their data with other programs and accept other program's data. We call this interface the Simple Script Wrapper (SSW). An implementation of SSW is shown that integrates groundwater, economic, and agricultural models in the High Plains region of Kansas. Output from these models illustrates the interdisciplinary discovery facilitated through use of SSW implemented models. Reference: Bulatewicz, T., A. Allen, J.M. Peterson, S. Staggenborg, S.M. Welch, and D.R. Steward, The Simple Script Wrapper for OpenMI: Enabling interdisciplinary modeling studies, Environmental Modelling & Software, 39, 283-294, 2013. http://dx.doi.org/10.1016/j.envsoft.2012.07.006 http://code.google.com/p/simple-script-wrapper/

Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

NASA Technical Reports Server (NTRS)

Wilson, Michael A.; Pohorille, Andrew

1991-01-01

Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

A Statistical Ontology-Based Approach to Ranking for Multiword Search

ERIC Educational Resources Information Center

Kim, Jinwoo

2013-01-01

Keyword search is a prominent data retrieval method for the Web, largely because the simple and efficient nature of keyword processing allows a large amount of information to be searched with fast response. However, keyword search approaches do not formally capture the clear meaning of a keyword query and fail to address the semantic relationships…

PmiRExAt: plant miRNA expression atlas database and web applications

PubMed Central

Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

2016-01-01

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

Précis of Simple heuristics that make us smart.

PubMed

Todd, P M; Gigerenzer, G

2000-10-01

How can anyone be rational in a world where knowledge is limited, time is pressing, and deep thought is often an unattainable luxury? Traditional models of unbounded rationality and optimization in cognitive science, economics, and animal behavior have tended to view decision-makers as possessing supernatural powers of reason, limitless knowledge, and endless time. But understanding decisions in the real world requires a more psychologically plausible notion of bounded rationality. In Simple heuristics that make us smart (Gigerenzer et al. 1999), we explore fast and frugal heuristics--simple rules in the mind's adaptive toolbox for making decisions with realistic mental resources. These heuristics can enable both living organisms and artificial systems to make smart choices quickly and with a minimum of information by exploiting the way that information is structured in particular environments. In this précis, we show how simple building blocks that control information search, stop search, and make decisions can be put together to form classes of heuristics, including: ignorance-based and one-reason decision making for choice, elimination models for categorization, and satisficing heuristics for sequential search. These simple heuristics perform comparably to more complex algorithms, particularly when generalizing to new data--that is, simplicity leads to robustness. We present evidence regarding when people use simple heuristics and describe the challenges to be addressed by this research program.

Microfluidic PMMA interfaces for rectangular glass capillaries

NASA Astrophysics Data System (ADS)

Evander, Mikael; Tenje, Maria

2014-02-01

We present the design and fabrication of a polymeric capillary fluidic interface fabricated by micro-milling. The design enables the use of glass capillaries with any kind of cross-section in complex microfluidic setups. We demonstrate two different designs of the interface; a double-inlet interface for hydrodynamic focusing and a capillary interface with integrated pneumatic valves. Both capillary interfaces are presented together with examples of practical applications. This communication shows the design optimization and presents details of the fabrication process. The capillary interface opens up for the use of complex microfluidic systems in single-use glass capillaries. They also enable simple fabrication of glass/polymer hybrid devices that can be beneficial in many research fields where a pure polymer chip negatively affects the device's performance, e.g. acoustofluidics.

An Open Port Sampling Interface for Liquid Introduction Atmospheric Pressure Ionization Mass Spectrometry

DOE PAGES

Van Berkel, Gary J.; Kertesz, Vilmos

2015-08-25

RATIONALE: A simple method to introduce unprocessed samples into a solvent for rapid characterization by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The continuous flow, self-cleaning open port sampling interface introduced here fills this void. METHODS: The open port sampling interface used a vertically aligned, co-axial tube arrangement enabling solvent delivery to the sampling end of the device through the tubing annulus and solvent aspiration down the center tube and into the mass spectrometer ionization source via the commercial APCI emitter probe. The solvent delivery rate to the interface was set to exceed the aspiration rate creatingmore » a continuous sampling interface along with a constant, self-cleaning spillover of solvent from the top of the probe. RESULTS: Using the open port sampling interface with positive ion mode APCI and a hybrid quadrupole time of flight mass spectrometer, rapid, direct sampling and analysis possibilities are exemplified with plastics, ballpoint and felt tip ink pens, skin, and vegetable oils. These results demonstrated that the open port sampling interface could be used as a simple, versatile and self-cleaning system to rapidly introduce multiple types of unprocessed, sometimes highly concentrated and complex, samples into a solvent flow stream for subsequent ionization and analysis by mass spectrometry. The basic setup presented here could be incorporated with any self-aspirating liquid introduction ionization source (e.g., ESI, APCI, APPI, ICP, etc.) or any type of atmospheric pressure sampling ready mass spectrometer system. CONCLUSIONS: The open port sampling interface provides a means to introduce and quickly analyze unprocessed solid or liquid samples with liquid introduction atmospheric pressure ionization source without fear of sampling interface or ionization source contamination.« less

A loosely coupled framework for terminology controlled distributed EHR search for patient cohort identification in clinical research.

PubMed

Zhao, Lei; Lim Choi Keung, Sarah N; Taweel, Adel; Tyler, Edward; Ogunsina, Ire; Rossiter, James; Delaney, Brendan C; Peterson, Kevin A; Hobbs, F D Richard; Arvanitis, Theodoros N

2012-01-01

Heterogeneous data models and coding schemes for electronic health records present challenges for automated search across distributed data sources. This paper describes a loosely coupled software framework based on the terminology controlled approach to enable the interoperation between the search interface and heterogeneous data sources. Software components interoperate via common terminology service and abstract criteria model so as to promote component reuse and incremental system evolution.

A simple procedure for the estimation of neutron skyshine from proton accelerators.

PubMed

Stevenson, G R; Thomas, R H

1984-01-01

Recent calculations of neutron diffusion at an air/ground interface have enabled the establishment of a very simple procedure for estimating neutron dose equivalent at large distances from proton accelerators in the energy range 10 MeV to several tens of GeV.

Inhibition of viscous fluid fingering: A variational scheme for optimal flow rates

NASA Astrophysics Data System (ADS)

Miranda, Jose; Dias, Eduardo; Alvarez-Lacalle, Enrique; Carvalho, Marcio

2012-11-01

Conventional viscous fingering flow in radial Hele-Shaw cells employs a constant injection rate, resulting in the emergence of branched interfacial shapes. The search for mechanisms to prevent the development of these bifurcated morphologies is relevant to a number of areas in science and technology. A challenging problem is how best to choose the pumping rate in order to restrain growth of interfacial amplitudes. We use an analytical variational scheme to look for the precise functional form of such an optimal flow rate. We find it increases linearly with time in a specific manner so that interface disturbances are minimized. Experiments and nonlinear numerical simulations support the effectiveness of this particularly simple, but not at all obvious, pattern controlling process. J.A.M., E.O.D. and M.S.C. thank CNPq/Brazil for financial support. E.A.L. acknowledges support from Secretaria de Estado de IDI Spain under project FIS2011-28820-C02-01.

Eye Tracking Based Control System for Natural Human-Computer Interaction

PubMed Central

Lin, Shu-Fan

2017-01-01

Eye movement can be regarded as a pivotal real-time input medium for human-computer communication, which is especially important for people with physical disability. In order to improve the reliability, mobility, and usability of eye tracking technique in user-computer dialogue, a novel eye control system with integrating both mouse and keyboard functions is proposed in this paper. The proposed system focuses on providing a simple and convenient interactive mode by only using user's eye. The usage flow of the proposed system is designed to perfectly follow human natural habits. Additionally, a magnifier module is proposed to allow the accurate operation. In the experiment, two interactive tasks with different difficulty (searching article and browsing multimedia web) were done to compare the proposed eye control tool with an existing system. The Technology Acceptance Model (TAM) measures are used to evaluate the perceived effectiveness of our system. It is demonstrated that the proposed system is very effective with regard to usability and interface design. PMID:29403528

Application of NASA Giovanni to Coastal Zone Remote Sensing Search

NASA Technical Reports Server (NTRS)

Acker, James; Leptoukh, Gregory; Kempler, Steven; Berrick, Stephen; Rui, Hualan; Shen, Suhung

2007-01-01

The Goddard Earth Sciences Data and Information Services Center (GES DISC) Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) provides rapid access to, and enables effective utilization of, remotely-sensed data that are applicable to investigations of coastal environmental processes. Data sets in Giovanni include precipitation data from the Tropical Rainfall Measuring Mission (TRMM), particularly useful for coastal storm investigations; ocean color radiometry data from the Sea-viewing Wide Field-of-view Sensor (SeaWIFS) and Moderate Resolution Imaging Spectroradiometer (MODIS), useful for water quality evaluation, phytoplankton blooms, and terrestrial-marine interactions; and atmospheric data from MODIS and the Advanced Infrared Sounder (AIRS), providing the capability to characterize atmospheric variables. Giovanni provides a simple interface allowing discovery and analysis of environmental data sets with accompanying graphic visualizations. Examples of Giovanni investigations of the coastal zone include hurricane and storm impacts, hydrologically-induced phytoplankton blooms, chlorophyll trend analysis, and dust storm characterization. New and near-future capabilities of Giovanni will be described.

SeqDepot: streamlined database of biological sequences and precomputed features.

PubMed

Ulrich, Luke E; Zhulin, Igor B

2014-01-15

Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot-a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to >28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines. Freely available on the web at http://seqdepot.net/. RESTaccess via http://seqdepot.net/api/v1. Database files and scripts maybe downloaded from http://seqdepot.net/download.

Eye Tracking Based Control System for Natural Human-Computer Interaction.

PubMed

Zhang, Xuebai; Liu, Xiaolong; Yuan, Shyan-Ming; Lin, Shu-Fan

2017-01-01

Eye movement can be regarded as a pivotal real-time input medium for human-computer communication, which is especially important for people with physical disability. In order to improve the reliability, mobility, and usability of eye tracking technique in user-computer dialogue, a novel eye control system with integrating both mouse and keyboard functions is proposed in this paper. The proposed system focuses on providing a simple and convenient interactive mode by only using user's eye. The usage flow of the proposed system is designed to perfectly follow human natural habits. Additionally, a magnifier module is proposed to allow the accurate operation. In the experiment, two interactive tasks with different difficulty (searching article and browsing multimedia web) were done to compare the proposed eye control tool with an existing system. The Technology Acceptance Model (TAM) measures are used to evaluate the perceived effectiveness of our system. It is demonstrated that the proposed system is very effective with regard to usability and interface design.

Data Integration Using SOAP in the VSO

NASA Astrophysics Data System (ADS)

Tian, K. Q.; Bogart, R. S.; Davey, A.; Dimitoglou, G.; Gurman, J. B.; Hill, F.; Martens, P. C.; Wampler, S.

2003-05-01

The Virtual Solar Observatory (VSO) project has implemented a time interval search for all four participating data archives. The back-end query services are implemented as web services, and are accessible via SOAP. SOAP (Simple Object Access Protocol) defines an RPC (Remote Procedure Call) mechanism that employs HTTP as its transport and encodes the client-server interactions (request and response messages) in XML (eXtensible Markup Language) documents. In addition to its core function of identifying relevant datasets in the local archive, the SOAP server at each data provider acts as a "wrapper" that maps descriptions in an abstract data model to those in the provider-specific data model, and vice versa. It is in this way that VSO integrates heterogeneous data services and allows access to them using a common interface. Our experience with SOAP has been fruitful. It has proven to be a better alternative to traditional web access methods, namely POST and GET, because of its flexibility and interoperability.

The Research and Implementation of Vehicle Bluetooth Hands-free Devices Key Parameters Downloading Algorithm

NASA Astrophysics Data System (ADS)

Zhang, Xiao-bo; Wang, Zhi-xue; Li, Jian-xin; Ma, Jian-hui; Li, Yang; Li, Yan-qiang

In order to facilitate Bluetooth function realization and information can be effectively tracked in the process of production, the vehicle Bluetooth hands-free devices need to download such key parameters as Bluetooth address, CVC license and base plate numbers, etc. Therefore, it is the aim to search simple and effective methods to download parameters for each vehicle Bluetooth hands-free device, and to control and record the use of parameters. In this paper, by means of Bluetooth Serial Peripheral Interface programmer device, the parallel port is switched to SPI. The first step is to download parameters is simulating SPI with the parallel port. To perform SPI function, operating the parallel port in accordance with the SPI timing. The next step is to achieve SPI data transceiver functions according to the programming parameters of options. Utilizing the new method, downloading parameters is fast and accurate. It fully meets vehicle Bluetooth hands-free devices production requirements. In the production line, it has played a large role.

A Comparison of Three Commercial Online Vendors.

ERIC Educational Resources Information Center

Hoover, Ryan E.

1979-01-01

Compares database update currency, number of hits, elapsed time, number of offline prints or online types, offline print turnaround time, vendor rates, total search cost, and discounted search cost based on vendor discount rates for five simple searches run on three major commercial vendors' online systems. (CWM)

The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

MyGeoHub: A Collaborative Geospatial Research and Education Platform

NASA Astrophysics Data System (ADS)

Kalyanam, R.; Zhao, L.; Biehl, L. L.; Song, C. X.; Merwade, V.; Villoria, N.

2017-12-01

Scientific research is increasingly collaborative and globally distributed; research groups now rely on web-based scientific tools and data management systems to simplify their day-to-day collaborative workflows. However, such tools often lack seamless interfaces, requiring researchers to contend with manual data transfers, annotation and sharing. MyGeoHub is a web platform that supports out-of-the-box, seamless workflows involving data ingestion, metadata extraction, analysis, sharing and publication. MyGeoHub is built on the HUBzero cyberinfrastructure platform and adds general-purpose software building blocks (GABBs), for geospatial data management, visualization and analysis. A data management building block iData, processes geospatial files, extracting metadata for keyword and map-based search while enabling quick previews. iData is pervasive, allowing access through a web interface, scientific tools on MyGeoHub or even mobile field devices via a data service API. GABBs includes a Python map library as well as map widgets that in a few lines of code, generate complete geospatial visualization web interfaces for scientific tools. GABBs also includes powerful tools that can be used with no programming effort. The GeoBuilder tool provides an intuitive wizard for importing multi-variable, geo-located time series data (typical of sensor readings, GPS trackers) to build visualizations supporting data filtering and plotting. MyGeoHub has been used in tutorials at scientific conferences and educational activities for K-12 students. MyGeoHub is also constantly evolving; the recent addition of Jupyter and R Shiny notebook environments enable reproducible, richly interactive geospatial analyses and applications ranging from simple pre-processing to published tools. MyGeoHub is not a monolithic geospatial science gateway, instead it supports diverse needs ranging from just a feature-rich data management system, to complex scientific tools and workflows.

Techniques for searching the CINAHL database using the EBSCO interface.

PubMed

Lawrence, Janna C

2007-04-01

The cumulative index to Nursing and Allied Health Literature (CINAHL) is a useful research tool for accessing articles of interest to nurses and health care professionals. More than 2,800 journals are indexed by CINAHL and can be searched easily using assigned subject headings. Detailed instructions about conducting, combining, and saving searches in CINAHL are provided in this article. Establishing an account at EBSCO further allows a nurse to save references and searches and to receive e-mail alerts when new articles on a topic of interest are published.

A Study of Search Intermediary Working Notes: Implications for IR System Design.

ERIC Educational Resources Information Center

Spink, Amanda; Goodrum, Abby

1996-01-01

Reports findings from an exploratory study investigating working notes created during encoding and external storage (EES) processes by human search intermediaries (librarians at the University of North Texas) using a Boolean information retrieval (IR) system. Implications for the design of IR interfaces and further research is discussed.…

The Specification of Causal Models with Tetrad IV: A Review

ERIC Educational Resources Information Center

Landsheer, J. A.

2010-01-01

Tetrad IV is a program designed for the specification of causal models. It is specifically designed to search for causal relations, but also offers the possibility to estimate the parameters of a structural equation model. It offers a remarkable graphical user interface, which facilitates building, evaluating, and searching for causal models. The…

SAO/NASA ADS at SAO: ADS Abstract Service

Science.gov Websites

Service provides a gateway to the online Astronomy and Physics literature. You can navigate this content filtering options as well as visualizations. Astronomy and Astrophysics Classic Search, an legacy interface which searches the 2,311,600 records currently in the Astronomy database, including 198,834 abstracts

A Smart Itsy Bitsy Spider for the Web.

ERIC Educational Resources Information Center

Chen, Hsinchun; Chung, Yi-Ming; Ramsey, Marshall; Yang, Christopher C.

1998-01-01

This study tested two Web personal spiders (i.e., agents that take users' requests and perform real-time customized searches) based on best first-search and genetic-algorithm techniques. Both results were comparable and complementary, although the genetic algorithm obtained higher recall value. The Java-based interface was found to be necessary…

Notes on Search, Detection and Localization Modeling. Revision 4

DTIC Science & Technology

1990-10-01

2, --- , k where the subregions are relabeled so that the following order relation holds: pi/6 1 > p 2!6 2 > ... > pr65 and where k is chosen so... Interfaces ," Operations Research, Vol. 19, No.3, pp 559-586, 1971. 15. Coggins, P.B., "Detection Probability Computations for Random Search of an

After Losing Users in Catalogs, Libraries Find Better Search Software

ERIC Educational Resources Information Center

Parry, Marc

2010-01-01

Traditional online library catalogs do not tend to order search results by ranked relevance, and they can befuddle users with clunky interfaces. However, that's changing because of two technology trends. First, a growing number of universities are shelling out serious money for sophisticated software that makes exploring their collections more…

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)

A Semiotic Analysis of Icons on the World Wide Web.

ERIC Educational Resources Information Center

Ma, Yan

The World Wide Web allows users to interact with a graphic interface to search information in a hypermedia and multimedia environment. Graphics serve as reference points on the World Wide Web for searching and retrieving information. This study analyzed the culturally constructed syntax patterns, or codes, embedded in the icons of library…

Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

NASA Astrophysics Data System (ADS)

Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

2017-08-01

We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar interfaces. We measure the normal and tangential components of the pressure tensor along the direction perpendicular to the interface and verify mechanical equilibrium of the two coexisting phases. In addition, we determine the non-equilibrium interfacial tension by integrating the difference of the normal and tangential components of the pressure tensor and show that the surface tension as a function of strength of particle attractions is well fitted by simple power laws. Finally, we measure the interfacial stiffness using capillary wave theory and the equipartition theorem and find a simple linear relation between surface tension and interfacial stiffness with a proportionality constant characterized by an effective temperature.

Control of the orbital ordering in manganite superlattices and impact on properties

NASA Astrophysics Data System (ADS)

Koçak, Ayşegül Begüm; Varignon, Julien; Lemal, Sébastien; Ghosez, Philippe; Lepetit, Marie-Bernadette

2017-09-01

The present paper theoretically studies the possibility to control the orbital ordering in manganite superlattices. Indeed, favored dz2eg -orbital occupancy is one of the proposed interpretations for the formation of a "dead" layer at the interfaces in manganite thin films and superlattices. We show here that favored dz2eg -orbital occupancy at the interfaces can be prevented by using alkaline-earth simple oxides as alternating layers in very thin superlattices. Such an alternating layer promotes the contraction of the manganite layers at the interfaces and favors a dx2-y2eg orbital occupancy. This result holds for different manganites, different alkaline-earth simple oxides, as well as different thicknesses of the two layers. While Boltzmann's transport calculations on different superlattices show unexpectedly only weak dependence of the electrical conductivity on the orbital ordering, the enhanced occupation of the dx2-y2 orbital should result in an increased Curie temperature.

Harmonised information exchange between decentralised food composition database systems.

PubMed

Pakkala, H; Christensen, T; de Victoria, I Martínez; Presser, K; Kadvan, A

2010-11-01

The main aim of the European Food Information Resource (EuroFIR) project is to develop and disseminate a comprehensive, coherent and validated data bank for the distribution of food composition data (FCD). This can only be accomplished by harmonising food description and data documentation and by the use of standardised thesauri. The data bank is implemented through a network of local FCD storages (usually national) under the control and responsibility of the local (national) EuroFIR partner. The implementation of the system based on the EuroFIR specifications is under development. The data interchange happens through the EuroFIR Web Services interface, allowing the partners to implement their system using methods and software suitable for the local computer environment. The implementation uses common international standards, such as Simple Object Access Protocol, Web Service Description Language and Extensible Markup Language (XML). A specifically constructed EuroFIR search facility (eSearch) was designed for end users. The EuroFIR eSearch facility compiles queries using a specifically designed Food Data Query Language and sends a request to those network nodes linked to the EuroFIR Web Services that will most likely have the requested information. The retrieved FCD are compiled into a specifically designed data interchange format (the EuroFIR Food Data Transport Package) in XML, which is sent back to the EuroFIR eSearch facility as the query response. The same request-response operation happens in all the nodes that have been selected in the EuroFIR eSearch facility for a certain task. Finally, the FCD are combined by the EuroFIR eSearch facility and delivered to the food compiler. The implementation of FCD interchange using decentralised computer systems instead of traditional data-centre models has several advantages. First of all, the local partners have more control over their FCD, which will increase commitment and improve quality. Second, a multicentred solution is more economically viable than the creation of a centralised data bank, because of the lack of national political support for multinational systems.

Locating Biodiversity Data Through The Global Change Master Directory

NASA Technical Reports Server (NTRS)

Olsen, Lola M.

1998-01-01

The Global Change Master Directory (GCMD) presently holds descriptions for almost 7000 data sets held worldwide. The directory's primary purpose is for data discovery. The information provided through the GCMD's Directory Interchange Format (DIF) is the set of information that a researcher would need to determine if a particular data set could be of value. By offering data set descriptions worldwide in many scientific disciplines - including meteorology, oceanography, ecology, geology, hydrology, geophysics, remote sensing, paleoclimate, solar-terrestrial physics, and human dimensions of climate change - the GCMD simplifies the discovery of data sources. Direct linkages to many of the data sets are also provided. In addition, several data set registration tools are offered for populating the directory. To search the directory, one may choose the Guided Search or Free-Text Search. Two experimental interfaces were also made available with the latest software release - one based on a keyword search and another based on a graphical interface. The graphical interface was designed in collaboration with the Human Computer Interaction Laboratory at the University of Maryland. The latest version of the software, Version 6, was released in April, 1998. It features the implementation of a scheme to handle hierarchical data set collections (parent-child relationships); a hierarchical geospatial location search scheme; a Java-based geographic map for conducting geospatial searches; a Related-URL field for project-related data set collections, metadata extensions (such as more detailed inventory information), etc.; a new implementation of the Isite software; a new dataset language field; hyperlinked email addresses, and more. The key to the continued evolution of the GCMD is in the flexibility of the GCMD database, allowing modifications and additions to made relatively easily to maintain currency, thus providing the ability to capitalize on current technology while importing all existing records. Changes are discussed and approved through an online "interoperability" forum. The next major release of the GCMD is scheduled for early 1999 and will include the incorporation of a new matrix-based interface, a rapid valids-based query system; improvement in the operations facility - important for future distributed options; new streamlined code for greater performance and maintainability; improvements in the handling of seven current fields proposed through the interoperability forum (at no expense to the data providers); and the release of DOCmorph, a more robust version of DIFmorph to translate many 'standards' multi-directionally. Issues and actions will also be addressed.

Computation of Acoustic Waves Through Sliding-Zone Interfaces Using an Euler/Navier-Stokes Code

NASA Technical Reports Server (NTRS)

Rumsey, Christopher L.

1996-01-01

The effect of a patched sliding-zone interface on the transmission of acoustic waves is examined for two- and three-dimensional model problems. A simple but general interpolation scheme at the patched boundary passes acoustic waves without distortion, provided that a sufficiently small time step is taken. A guideline is provided for the maximum permissible time step or zone speed that gives an acceptable error introduced by the sliding-zone interface.

Interface design principles for high-performance organic semiconductor devices

DOE PAGES

Nie, Wanyi; Gupta, Gautam; Crone, Brian K.; ...

2015-03-23

Organic solar cells (OSCs) are a promising cost-effective candidate in next generation photovoltaic technology. However, a critical bottleneck for OSCs is the electron/hole recombination loss through charge transfer state at the interface, which greatly limits the power conversion efficiency. W. Nie, A. Mohite, and co-workers demonstrate a simple strategy of suppressing the recombination rate by inserting a spacer layer at the donor-acceptor interface, resulting in a dramatic increase in power conversion efficiency.

Interface Circuits for Self-Checking Microprocessors

NASA Technical Reports Server (NTRS)

Rennels, D. A.; Chandramouli, R.

1986-01-01

Fault-tolerant-microcomputer concept based on enhancing "simple" computer with redundancy and self-checking logic circuits detect hardware faults. Interface and checking logic and redundant processors confer on 16-bit microcomputer ability to check itself for hardware faults. Checking circuitry also checks itself. Concept of self-checking complementary pairs (SCCP's) employed throughout ICL unit.

Using R in Introductory Statistics Courses with the pmg Graphical User Interface

ERIC Educational Resources Information Center

Verzani, John

2008-01-01

The pmg add-on package for the open source statistics software R is described. This package provides a simple to use graphical user interface (GUI) that allows introductory statistics students, without advanced computing skills, to quickly create the graphical and numeric summaries expected of them. (Contains 9 figures.)

Noninvasive control of dental calculus removal: qualification of two fluorescence methods

NASA Astrophysics Data System (ADS)

Gonchukov, S.; Sukhinina, A.; Bakhmutov, D.; Biryukova, T.

2013-02-01

The main condition of periodontitis prevention is the full calculus removal from the teeth surface. This procedure should be fulfilled without harming adjacent unaffected tooth tissues. Nevertheless the problem of sensitive and precise estimating of tooth-calculus interface exists and potential risk of hard tissue damage remains. In this work it was shown that fluorescence diagnostics during calculus removal can be successfully used for precise noninvasive detection of calculus-tooth interface. In so doing the simple implementation of this method free from the necessity of spectrometer using can be employed. Such a simple implementation of calculus detection set-up can be aggregated with the devices of calculus removing.

Influence of social presence on eye movements in visual search tasks.

PubMed

Liu, Na; Yu, Ruifeng

2017-12-01

This study employed an eye-tracking technique to investigate the influence of social presence on eye movements in visual search tasks. A total of 20 male subjects performed visual search tasks in a 2 (target presence: present vs. absent) × 2 (task complexity: complex vs. simple) × 2 (social presence: alone vs. a human audience) within-subject experiment. Results indicated that the presence of an audience could evoke a social facilitation effect on response time in visual search tasks. Compared with working alone, the participants made fewer and shorter fixations, larger saccades and shorter scan path in simple search tasks and more and longer fixations, smaller saccades and longer scan path in complex search tasks when working with an audience. The saccade velocity and pupil diameter in the audience-present condition were larger than those in the working-alone condition. No significant change in target fixation number was observed between two social presence conditions. Practitioner Summary: This study employed an eye-tracking technique to examine the influence of social presence on eye movements in visual search tasks. Results clarified the variation mechanism and characteristics of oculomotor scanning induced by social presence in visual search.

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

Creating a Classroom Kaleidoscope with the World Wide Web.

ERIC Educational Resources Information Center

Quinlan, Laurie A.

1997-01-01

Discusses the elements of classroom Web presentations: planning; construction, including design tips; classroom use; and assessment. Lists 14 World Wide Web resources for K-12 teachers; Internet search tools (directories, search engines and meta-search engines); a Web glossary; and an example of HTML for a simple Web page. (PEN)

A Simple Interactive Software Package for Plotting, Animating, and Calculating

ERIC Educational Resources Information Center

Engelhardt, Larry

2012-01-01

We introduce a new open source (free) software package that provides a simple, highly interactive interface for carrying out certain mathematical tasks that are commonly encountered in physics. These tasks include plotting and animating functions, solving systems of coupled algebraic equations, and basic calculus (differentiating and integrating…

The wisdom of crowds for visual search

PubMed Central

Juni, Mordechai Z.; Eckstein, Miguel P.

2017-01-01

Decision-making accuracy typically increases through collective integration of people’s judgments into group decisions, a phenomenon known as the wisdom of crowds. For simple perceptual laboratory tasks, classic signal detection theory specifies the upper limit for collective integration benefits obtained by weighted averaging of people’s confidences, and simple majority voting can often approximate that limit. Life-critical perceptual decisions often involve searching large image data (e.g., medical, security, and aerial imagery), but the expected benefits and merits of using different pooling algorithms are unknown for such tasks. Here, we show that expected pooling benefits are significantly greater for visual search than for single-location perceptual tasks and the prediction given by classic signal detection theory. In addition, we show that simple majority voting obtains inferior accuracy benefits for visual search relative to averaging and weighted averaging of observers’ confidences. Analysis of gaze behavior across observers suggests that the greater collective integration benefits for visual search arise from an interaction between the foveated properties of the human visual system (high foveal acuity and low peripheral acuity) and observers’ nonexhaustive search patterns, and can be predicted by an extended signal detection theory framework with trial to trial sampling from a varying mixture of high and low target detectabilities across observers (SDT-MIX). These findings advance our theoretical understanding of how to predict and enhance the wisdom of crowds for real world search tasks and could apply more generally to any decision-making task for which the minority of group members with high expertise varies from decision to decision. PMID:28490500

Characteristic power spectrum of diffusive interface dynamics in the two-dimensional Ising model

NASA Astrophysics Data System (ADS)

Masumoto, Yusuke; Takesue, Shinji

2018-05-01

We investigate properties of the diffusive motion of an interface in the two-dimensional Ising model in equilibrium or nonequilibrium situations. We focused on the relation between the power spectrum of a time sequence of spins and diffusive motion of an interface which was already clarified in one-dimensional systems with a nonequilibrium phase transition like the asymmetric simple exclusion process. It is clarified that the interface motion is a diffusion process with a drift force toward the higher-temperature side when the system is in contact with heat reservoirs at different temperatures and heat transfers through the system. Effects of the width of the interface are also discussed.

Improving the User Experience of Finding and Visualizing Oceanographic Data

NASA Astrophysics Data System (ADS)

Rauch, S.; Allison, M. D.; Groman, R. C.; Chandler, C. L.; Galvarino, C.; Gegg, S. R.; Kinkade, D.; Shepherd, A.; Wiebe, P. H.; Glover, D. M.

2013-12-01

Searching for and locating data of interest can be a challenge to researchers as increasing volumes of data are made available online through various data centers, repositories, and archives. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is keenly aware of this challenge and, as a result, has implemented features and technologies aimed at improving data discovery and enhancing the user experience. BCO-DMO was created in 2006 to manage and publish data from research projects funded by the Division of Ocean Sciences (OCE) Biological and Chemical Oceanography Sections and the Division of Polar Programs (PLR) Antarctic Sciences Organisms and Ecosystems Program (ANT) of the US National Science Foundation (NSF). The BCO-DMO text-based and geospatial-based data access systems provide users with tools to search, filter, and visualize data in order to efficiently find data of interest. The geospatial interface, developed using a suite of open-source software (including MapServer [1], OpenLayers [2], ExtJS [3], and MySQL [4]), allows users to search and filter/subset metadata based on program, project, or deployment, or by using a simple word search. The map responds based on user selections, presents options that allow the user to choose specific data parameters (e.g., a species or an individual drifter), and presents further options for visualizing those data on the map or in "quick-view" plots. The data managed and made available by BCO-DMO are very heterogeneous in nature, from in-situ biogeochemical, ecological, and physical data, to controlled laboratory experiments. Due to the heterogeneity of the data types, a 'one size fits all' approach to visualization cannot be applied. Datasets are visualized in a way that will best allow users to assess fitness for purpose. An advanced geospatial interface, which contains a semantically-enabled faceted search [5], is also available. These search facets are highly interactive and responsive, allowing users to construct their own custom searches by applying multiple filters. New filtering and visualization tools are continually being added to the BCO-DMO system as new data types are encountered and as we receive feedback from our data contributors and users. As our system becomes more complex, teaching users about the many interactive features becomes increasingly important. Tutorials and videos are made available online. Recent in-person classroom-style tutorials have proven useful for both demonstrating our system to users and for obtaining feedback to further improve the user experience. References: [1] University of Minnesota. MapServer: Open source web mapping. http://www.mapserver.org [2] OpenLayers: Free Maps for the Web. http://www.openlayers.org [3] Sencha. ExtJS. http://www.sencha.com/products/extjs [4] MySQL. http://www.mysql.com/ [5] Maffei, A. R., Rozell, E. A., West, P., Zednik, S., and Fox, P. A. 2011. Open Standards and Technologies in the S2S Framework. Abstract IN31A-1435 presented at American Geophysical Union 2011 Fall Meeting, San Francisco, CA, 7 December 2011.

Semantic interpretation of search engine resultant

NASA Astrophysics Data System (ADS)

Nasution, M. K. M.

2018-01-01

In semantic, logical language can be interpreted in various forms, but the certainty of meaning is included in the uncertainty, which directly always influences the role of technology. One results of this uncertainty applies to search engines as user interfaces with information spaces such as the Web. Therefore, the behaviour of search engine results should be interpreted with certainty through semantic formulation as interpretation. Behaviour formulation shows there are various interpretations that can be done semantically either temporary, inclusion, or repeat.

MyMolDB: a micromolecular database solution with open source and free components.

PubMed

Xia, Bing; Tai, Zheng-Fu; Gu, Yu-Cheng; Li, Bang-Jing; Ding, Li-Sheng; Zhou, Yan

2011-10-01

To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open-source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open-source solution to manage chemicals in research groups based on open source and free components. It has a user-friendly interface with the functions of chemical handling and intensive searching. MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web-based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching. MyMolDB is an open-source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/. Copyright © 2011 Wiley Periodicals, Inc.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

PubMed

Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

2018-01-04

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

Simple heuristics in over-the-counter drug choices: a new hint for medical education and practice.

PubMed

Riva, Silvia; Monti, Marco; Antonietti, Alessandro

2011-01-01

Over-the-counter (OTC) drugs are widely available and often purchased by consumers without advice from a health care provider. Many people rely on self-management of medications to treat common medical conditions. Although OTC medications are regulated by the National and the International Health and Drug Administration, many people are unaware of proper dosing, side effects, adverse drug reactions, and possible medication interactions. This study examined how subjects make their decisions to select an OTC drug, evaluating the role of cognitive heuristics which are simple and adaptive rules that help the decision-making process of people in everyday contexts. By analyzing 70 subjects' information-search and decision-making behavior when selecting OTC drugs, we examined the heuristics they applied in order to assess whether simple decision-making processes were also accurate and relevant. Subjects were tested with a sequence of two experimental tests based on a computerized Java system devised to analyze participants' choices in a virtual environment. We found that subjects' information-search behavior reflected the use of fast and frugal heuristics. In addition, although the heuristics which correctly predicted subjects' decisions implied significantly fewer cues on average than the subjects did in the information-search task, they were accurate in describing order of information search. A simple combination of a fast and frugal tree and a tallying rule predicted more than 78% of subjects' decisions. The current emphasis in health care is to shift some responsibility onto the consumer through expansion of self medication. To know which cognitive mechanisms are behind the choice of OTC drugs is becoming a relevant purpose of current medical education. These findings have implications both for the validity of simple heuristics describing information searches in the field of OTC drug choices and for current medical education, which has to prepare competent health specialists to orientate and support the choices of their patients.

Simple heuristics in over-the-counter drug choices: a new hint for medical education and practice

PubMed Central

Riva, Silvia; Monti, Marco; Antonietti, Alessandro

2011-01-01

Introduction Over-the-counter (OTC) drugs are widely available and often purchased by consumers without advice from a health care provider. Many people rely on self-management of medications to treat common medical conditions. Although OTC medications are regulated by the National and the International Health and Drug Administration, many people are unaware of proper dosing, side effects, adverse drug reactions, and possible medication interactions. Purpose This study examined how subjects make their decisions to select an OTC drug, evaluating the role of cognitive heuristics which are simple and adaptive rules that help the decision-making process of people in everyday contexts. Subjects and methods By analyzing 70 subjects’ information-search and decision-making behavior when selecting OTC drugs, we examined the heuristics they applied in order to assess whether simple decision-making processes were also accurate and relevant. Subjects were tested with a sequence of two experimental tests based on a computerized Java system devised to analyze participants’ choices in a virtual environment. Results We found that subjects’ information-search behavior reflected the use of fast and frugal heuristics. In addition, although the heuristics which correctly predicted subjects’ decisions implied significantly fewer cues on average than the subjects did in the information-search task, they were accurate in describing order of information search. A simple combination of a fast and frugal tree and a tallying rule predicted more than 78% of subjects’ decisions. Conclusion The current emphasis in health care is to shift some responsibility onto the consumer through expansion of self medication. To know which cognitive mechanisms are behind the choice of OTC drugs is becoming a relevant purpose of current medical education. These findings have implications both for the validity of simple heuristics describing information searches in the field of OTC drug choices and for current medical education, which has to prepare competent health specialists to orientate and support the choices of their patients. PMID:23745077

Bio-inspired Edible Superhydrophobic Interface for Reducing Residual Liquid Food.

PubMed

Li, Yao; Bi, Jingran; Wang, Siqi; Zhang, Tan; Xu, Xiaomeng; Wang, Haitao; Cheng, Shasha; Zhu, Bei-Wei; Tan, Mingqian

2018-03-07

Significant wastage of residual liquid food, such as milk, yogurt, and honey, in food containers has attracted great attention. In this work, a bio-inspired edible superhydrophobic interface was fabricated using U.S. Food and Drug Administration-approved and edible honeycomb wax, arabic gum, and gelatin by a simple and low-cost method. The bio-inspired edible superhydrophobic interface showed multiscale structures, which were similar to that of a lotus leaf surface. This bio-inspired edible superhydrophobic interface displayed high contact angles for a variety of liquid foods, and the residue of liquid foods could be effectively reduced using the bio-inspired interface. To improve the adhesive force of the superhydrophobic interface, a flexible edible elastic film was fabricated between the interface and substrate material. After repeated folding and flushing for a long time, the interface still maintained excellent superhydrophobic property. The bio-inspired edible superhydrophobic interface showed good biocompatibility, which may have potential applications as a functional packaging interface material.

Using Natural Language to Enable Mission Managers to Control Multiple Heterogeneous UAVs

NASA Technical Reports Server (NTRS)

Trujillo, Anna C.; Puig-Navarro, Javier; Mehdi, S. Bilal; Mcquarry, A. Kyle

2016-01-01

The availability of highly capable, yet relatively cheap, unmanned aerial vehicles (UAVs) is opening up new areas of use for hobbyists and for commercial activities. This research is developing methods beyond classical control-stick pilot inputs, to allow operators to manage complex missions without in-depth vehicle expertise. These missions may entail several heterogeneous UAVs flying coordinated patterns or flying multiple trajectories deconflicted in time or space to predefined locations. This paper describes the functionality and preliminary usability measures of an interface that allows an operator to define a mission using speech inputs. With a defined and simple vocabulary, operators can input the vast majority of mission parameters using simple, intuitive voice commands. Although the operator interface is simple, it is based upon autonomous algorithms that allow the mission to proceed with minimal input from the operator. This paper also describes these underlying algorithms that allow an operator to manage several UAVs.

Quantum search of a real unstructured database

NASA Astrophysics Data System (ADS)

Broda, Bogusław

2016-02-01

A simple circuit implementation of the oracle for Grover's quantum search of a real unstructured classical database is proposed. The oracle contains a kind of quantumly accessible classical memory, which stores the database.

Self-assembling fluidic machines

NASA Astrophysics Data System (ADS)

Grzybowski, Bartosz A.; Radkowski, Michal; Campbell, Christopher J.; Lee, Jessamine Ng; Whitesides, George M.

2004-03-01

This letter describes dynamic self-assembly of two-component rotors floating at the interface between liquid and air into simple, reconfigurable mechanical systems ("machines"). The rotors are powered by an external, rotating magnetic field, and their positions within the interface are controlled by: (i) repulsive hydrodynamic interactions between them and (ii) by localized magnetic fields produced by an array of small electromagnets located below the plane of the interface. The mechanical functions of the machines depend on the spatiotemporal sequence of activation of the electromagnets.

An object oriented implementation of the Yeadon human inertia model

PubMed Central

Dembia, Christopher; Moore, Jason K.; Hubbard, Mont

2015-01-01

We present an open source software implementation of a popular mathematical method developed by M.R. Yeadon for calculating the body and segment inertia parameters of a human body. The software is written in a high level open source language and provides three interfaces for manipulating the data and the model: a Python API, a command-line user interface, and a graphical user interface. Thus the software can fit into various data processing pipelines and requires only simple geometrical measures as input. PMID:25717365

An object oriented implementation of the Yeadon human inertia model.

PubMed

Dembia, Christopher; Moore, Jason K; Hubbard, Mont

2014-01-01

We present an open source software implementation of a popular mathematical method developed by M.R. Yeadon for calculating the body and segment inertia parameters of a human body. The software is written in a high level open source language and provides three interfaces for manipulating the data and the model: a Python API, a command-line user interface, and a graphical user interface. Thus the software can fit into various data processing pipelines and requires only simple geometrical measures as input.

Nested Dissection Interface Reconstruction in Pececillo

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

Jibben, Zechariah Joel

A nested dissection method for interface reconstruction in a volume tracking framework has been implemented in Pececillo. This method provides a significant improvement over the traditional onion-skin method, which does not appropriately handle T-shaped multimaterial intersections and dynamic contact lines present in additive manufacturing simulations. The resulting implementation lays the groundwork for further re- search in numerical contact angle estimates.

Impact of the type of mask on the effectiveness of and adherence to continuous positive airway pressure treatment for obstructive sleep apnea.

PubMed

Andrade, Rafaela Garcia Santos de; Piccin, Vivien Schmeling; Nascimento, Juliana Araújo; Viana, Fernanda Madeiro Leite; Genta, Pedro Rodrigues; Lorenzi-Filho, Geraldo

2014-01-01

Continuous positive airway pressure (CPAP) is the gold standard for the treatment of obstructive sleep apnea (OSA). Although CPAP was originally applied with a nasal mask, various interfaces are currently available. This study reviews theoretical concepts and questions the premise that all types of interfaces produce similar results. We revised the evidence in the literature about the impact that the type of CPAP interface has on the effectiveness of and adherence to OSA treatment. We searched the PubMed database using the search terms "CPAP", "mask", and "obstructive sleep apnea". Although we identified 91 studies, only 12 described the impact of the type of CPAP interface on treatment effectiveness (n = 6) or adherence (n = 6). Despite conflicting results, we found no consistent evidence that nasal pillows and oral masks alter OSA treatment effectiveness or adherence. In contrast, most studies showed that oronasal masks are less effective and are more often associated with lower adherence and higher CPAP abandonment than are nasal masks. We concluded that oronasal masks can compromise CPAP OSA treatment adherence and effectiveness. Further studies are needed in order to understand the exact mechanisms involved in this effect.

Impact of the type of mask on the effectiveness of and adherence to continuous positive airway pressure treatment for obstructive sleep apnea*

PubMed Central

de Andrade, Rafaela Garcia Santos; Piccin, Vivien Schmeling; Nascimento, Juliana Araújo; Viana, Fernanda Madeiro Leite; Genta, Pedro Rodrigues; Lorenzi-Filho, Geraldo

2014-01-01

Continuous positive airway pressure (CPAP) is the gold standard for the treatment of obstructive sleep apnea (OSA). Although CPAP was originally applied with a nasal mask, various interfaces are currently available. This study reviews theoretical concepts and questions the premise that all types of interfaces produce similar results. We revised the evidence in the literature about the impact that the type of CPAP interface has on the effectiveness of and adherence to OSA treatment. We searched the PubMed database using the search terms "CPAP", "mask", and "obstructive sleep apnea". Although we identified 91 studies, only 12 described the impact of the type of CPAP interface on treatment effectiveness (n = 6) or adherence (n = 6). Despite conflicting results, we found no consistent evidence that nasal pillows and oral masks alter OSA treatment effectiveness or adherence. In contrast, most studies showed that oronasal masks are less effective and are more often associated with lower adherence and higher CPAP abandonment than are nasal masks. We concluded that oronasal masks can compromise CPAP OSA treatment adherence and effectiveness. Further studies are needed in order to understand the exact mechanisms involved in this effect. PMID:25610507

The Reactome pathway Knowledgebase

PubMed Central

Fabregat, Antonio; Sidiropoulos, Konstantinos; Garapati, Phani; Gillespie, Marc; Hausmann, Kerstin; Haw, Robin; Jassal, Bijay; Jupe, Steven; Korninger, Florian; McKay, Sheldon; Matthews, Lisa; May, Bruce; Milacic, Marija; Rothfels, Karen; Shamovsky, Veronica; Webber, Marissa; Weiser, Joel; Williams, Mark; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, Peter

2016-01-01

The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently. PMID:26656494

Curating the Web: Building a Google Custom Search Engine for the Arts

ERIC Educational Resources Information Center

Hennesy, Cody; Bowman, John

2008-01-01

Google's first foray onto the web made search simple and results relevant. With its Co-op platform, Google has taken another step toward dramatically increasing the relevancy of search results, further adapting the World Wide Web to local needs. Google Custom Search Engine, a tool on the Co-op platform, puts one in control of his or her own search…

Preference vs. Authority: A Comparison of Student Searching in a Subject-Specific Indexing and Abstracting Database and a Customized Discovery Layer

ERIC Educational Resources Information Center

Dahlen, Sarah P. C.; Hanson, Kathlene

2017-01-01

Discovery layers provide a simplified interface for searching library resources. Libraries with limited finances make decisions about retaining indexing and abstracting databases when similar information is available in discovery layers. These decisions should be informed by student success at finding quality information as well as satisfaction…

Application developer's tutorial for the CSM testbed architecture

NASA Technical Reports Server (NTRS)

Underwood, Phillip; Felippa, Carlos A.

1988-01-01

This tutorial serves as an illustration of the use of the programmer interface on the CSM Testbed Architecture (NICE). It presents a complete, but simple, introduction to using both the GAL-DBM (Global Access Library-Database Manager) and CLIP (Command Language Interface Program) to write a NICE processor. Familiarity with the CSM Testbed architecture is required.

Preparing Content-Rich Learning Environments with VPython and Excel, Controlled by Visual Basic for Applications

ERIC Educational Resources Information Center

Prayaga, Chandra

2008-01-01

A simple interface between VPython and Microsoft (MS) Office products such as Word and Excel, controlled by Visual Basic for Applications, is described. The interface allows the preparation of content-rich, interactive learning environments by taking advantage of the three-dimensional (3D) visualization capabilities of VPython and the GUI…

Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis.

PubMed

Kremer, Lukas P M; Leufken, Johannes; Oyunchimeg, Purevdulam; Schulze, Stefan; Fufezan, Christian

2016-03-04

Proteomics data integration has become a broad field with a variety of programs offering innovative algorithms to analyze increasing amounts of data. Unfortunately, this software diversity leads to many problems as soon as the data is analyzed using more than one algorithm for the same task. Although it was shown that the combination of multiple peptide identification algorithms yields more robust results, it is only recently that unified approaches are emerging; however, workflows that, for example, aim to optimize search parameters or that employ cascaded style searches can only be made accessible if data analysis becomes not only unified but also and most importantly scriptable. Here we introduce Ursgal, a Python interface to many commonly used bottom-up proteomics tools and to additional auxiliary programs. Complex workflows can thus be composed using the Python scripting language using a few lines of code. Ursgal is easily extensible, and we have made several database search engines (X!Tandem, OMSSA, MS-GF+, Myrimatch, MS Amanda), statistical postprocessing algorithms (qvality, Percolator), and one algorithm that combines statistically postprocessed outputs from multiple search engines ("combined FDR") accessible as an interface in Python. Furthermore, we have implemented a new algorithm ("combined PEP") that combines multiple search engines employing elements of "combined FDR", PeptideShaker, and Bayes' theorem.

Space tug/shuttle interface compatibility study. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1975-01-01

Shuttle interfaces required for space tug accommodation are primarily involved with supporting and servicing the tug during launch countdown, flight, and postlanding; deploying and retrieving the tug on orbit; and maintaining control over the tug when it is in or near the orbiter. Each of these interface areas was investigated to determine the best physical and operational method of accomplishing the required functions, with an overriding goal of establishing simple and flexible orbiter interface requirements suitable for tug, tug payloads, IUS and other cargo. It is concluded the orbiter payload accommodations and the MSFC baseline tug are generally interface compatible. Specific minor changes to tug and orbiter interfaces were identified to provide full compatibility. A system concept for supporting and deploying tug from orbiter is described.

Graphical programming interface: A development environment for MRI methods.

PubMed

Zwart, Nicholas R; Pipe, James G

2015-11-01

To introduce a multiplatform, Python language-based, development environment called graphical programming interface for prototyping MRI techniques. The interface allows developers to interact with their scientific algorithm prototypes visually in an event-driven environment making tasks such as parameterization, algorithm testing, data manipulation, and visualization an integrated part of the work-flow. Algorithm developers extend the built-in functionality through simple code interfaces designed to facilitate rapid implementation. This article shows several examples of algorithms developed in graphical programming interface including the non-Cartesian MR reconstruction algorithms for PROPELLER and spiral as well as spin simulation and trajectory visualization of a FLORET example. The graphical programming interface framework is shown to be a versatile prototyping environment for developing numeric algorithms used in the latest MR techniques. © 2014 Wiley Periodicals, Inc.

The connector space reduction mechanism

NASA Technical Reports Server (NTRS)

Milam, M. Bruce

1990-01-01

The Connector Space Reduction Mechanism (CSRM) is a simple device that can reduce the number of electromechanical devices on the Payload Interface Adapter/Station Interface Adapter (PIA/SIA) from 4 to 1. The device uses simplicity to attack the heart of the connector mating problem for large interfaces. The CSRM allows blind mate connector mating with minimal alignment required over short distances. This eliminates potential interface binding problems and connector damage. The CSRM is compatible with G and H connectors and Moog Rotary Shutoff fluid couplings. The CSRM can be used also with less forgiving connectors, as was demonstrated in the lab. The CSRM is NASA-Goddard exclusive design with patent applied for. The CSRM is the correct mechanism for the PIA/SIA interface as well as other similar berthing interfaces.

Planet Hunters 2 in the K2 Era

NASA Astrophysics Data System (ADS)

Schwamb, Megan E.; Fischer, Debra; Boyajian, Tabetha S.; Giguere, Matthew J.; Ishikawa, Sascha; Lintott, Chris; Lynn, Stuart; Schmitt, Joseph; Snyder, Chris; Wang, Ji; Barclay, Thomas

2015-01-01

Planet Hunters (http://www.planethunters.org) is an online citizen science project enlisting hundreds of thousands of people to search for planet transits in the publicly released Kepler data. Volunteers mark the locations of visible transits in a web interface, with multiple independent classifiers reviewing a randomly selected ~30-day light curve segment. In September 2014, Planet Hunters entered a new phase. The project was relaunched with a brand new online classification interface and discussion tool built using the Zooniverse's (http://www.zooniverse.org) latest technology and web platform. The website has been optimized for the rapid discovery and identification of planet candidates in the light curves from K2, the two-wheeled ecliptic plane Kepler mission. We will give an overview of the new Planet Hunters classification interface and Round 2 review system in context of the K2 data. We will present the first results from the Planet Hunters 2 search of K2 Campaigns 0 and 1 including a summary of new planet candidates.

The Virtual Solar Observatory: What Are We Up To Now?

NASA Technical Reports Server (NTRS)

Gurman, J. B.; Hill, F.; Suarez-Sola, F.; Bogart, R.; Amezcua, A.; Martens, P.; Hourcle, J.; Hughitt, K.; Davey, A.

2012-01-01

In the nearly ten years of a functional Virtual Solar Observatory (VSO), http://virtualsolar.org/ we have made it possible to query and access sixty-seven distinct solar data products and several event lists from nine spacecraft and fifteen observatories or observing networks. We have used existing VSO technology, and developed new software, for a distributed network of sites caching and serving SDO HMI and/ or AlA data. We have also developed an application programming interface (API) that has enabled VSO search and data access capabilities in IDL, Python, and Java. We also have quite a bit of work yet to do, including completion of the implementation of access to SDO EVE data, and access to some nineteen other data sets from space- and ground-based observatories. In addition, we have been developing a new graphic user interface that will enable the saving of user interface and search preferences. We solicit advice from the community input prioritizing our task list, and adding to it

Active Ingredient - AZ

EPA Pesticide Factsheets

EPA Pesticide Chemical Search allows a user to easily find the pesticide chemical or active ingredient that they are interested in by using an array of simple to advanced search options. Chemical Search provides a single point of reference for easy access to information previously published in a variety of locations, including various EPA web pages and Regulations.gov.

An Impact-Based Filtering Approach for Literature Searches

ERIC Educational Resources Information Center

Vista, Alvin

2013-01-01

This paper aims to present an alternative and simple method to improve the filtering of search results so as to increase the efficiency of literature searches, particularly for individual researchers who have limited logistical resources. The method proposed here is scope restriction using an impact-based filter, made possible by the emergence of…

Mortality estimation from carcass searches using the R-package carcass – a tutorial

EPA Science Inventory

This article is a tutorial for the R-package carcass. It starts with a short overview of common methods used to estimate mortality based on carcass searches. Then, it guides step by step through a simple example. First, the proportion of animals that fall into the search area is ...

Exploratory power of the harmony search algorithm: analysis and improvements for global numerical optimization.

PubMed

Das, Swagatam; Mukhopadhyay, Arpan; Roy, Anwit; Abraham, Ajith; Panigrahi, Bijaya K

2011-02-01

The theoretical analysis of evolutionary algorithms is believed to be very important for understanding their internal search mechanism and thus to develop more efficient algorithms. This paper presents a simple mathematical analysis of the explorative search behavior of a recently developed metaheuristic algorithm called harmony search (HS). HS is a derivative-free real parameter optimization algorithm, and it draws inspiration from the musical improvisation process of searching for a perfect state of harmony. This paper analyzes the evolution of the population-variance over successive generations in HS and thereby draws some important conclusions regarding the explorative power of HS. A simple but very useful modification to the classical HS has been proposed in light of the mathematical analysis undertaken here. A comparison with the most recently published variants of HS and four other state-of-the-art optimization algorithms over 15 unconstrained and five constrained benchmark functions reflects the efficiency of the modified HS in terms of final accuracy, convergence speed, and robustness.

TSAFE Interface Control Document v 2.0

NASA Technical Reports Server (NTRS)

Paielli, Russell A.; Bach, Ralph E.

2013-01-01

This document specifies the data interface for TSAFE, the Tactical Separation-Assured Flight Environment. TSAFE is a research prototype of a software application program for alerting air traffic controllers to imminent conflicts in enroute airspace. It is intended for Air Route Traffic Control Centers ("Centers") in the U.S. National Airspace System. It predicts trajectories for approximately 3 minutes into the future, searches for conflicts, and sends data about predicted conflicts to the client, which uses the data to alert an air traffic controller of conflicts. TSAFE itself does not provide a graphical user interface.

ScienceDirect through SciVerse: a new way to approach Elsevier.

PubMed

Bengtson, Jason

2011-01-01

SciVerse is the new combined portal from Elsevier that services their ScienceDirect collection, SciTopics, and their Scopus database. Using SciVerse to access ScienceDirect is the specific focus of this review. Along with advanced keyword searching and citation searching options, SciVerse also incorporates a very useful image search feature. The aim seems to be not only to create an interface that provides broad functionality on par with other database search tools that many searchers use regularly but also to create an open platform that could be changed to respond effectively to the needs of customers.

Constructing Uniform Resource Locators (URLs) for Searching the Marine Realms Information Bank

USGS Publications Warehouse

Linck, Guthrie A.; Allwardt, Alan O.; Lightsom, Frances L.

2009-01-01

The Marine Realms Information Bank (MRIB) is a digital library that provides access to free online scientific information about the oceans and coastal regions. To search its collection, MRIB uses a Common Gateway Interface (CGI) program, which allows automated search requests using Uniform Resource Locators (URLs). This document provides an overview of how to construct URLs to execute MRIB queries. The parameters listed allow detailed control of which records are retrieved, how they are returned, and how their display is formatted.

[Fluorescence control of dental calculus removal].

PubMed

Bakhmutov, D N; Gonchukov, S A; Lonkina, T V; Sukhinina, A V

2012-01-01

The main condition of periodontitis prevention is the full calculus removal from the teeth surface. This procedure should be fulfilled without harming adjacent unaffected tooth tissues. Nevertheless the problem of sensitive and precise estimating of tooth-calculus interface exists and potential risk of hard tissue damage remains. In the frames of this work it was shown that fluorescence diagnostics during calculus removal can be successfully used for precise detection of tooth-calculus interface. In so doing the simple implementation of this method free from the necessity of spectrometer using can be employed. Such a simple implementation of calculus detection set-up can be aggregated with the devices of calculus removing (as ultrasonic or laser devices).

Copper phthalocyanine films deposited by liquid-liquid interface recrystallization technique (LLIRCT).

PubMed

Patil, K R; Sathaye, S D; Hawaldar, R; Sathe, B R; Mandale, A B; Mitra, A

2007-11-15

The simple recrystallization process is innovatively used to obtain the nanoparticles of copper phthalocyanine by a simple method. Liquid-liquid interface recrystallization technique (LLIRCT) has been employed successfully to produce small sized copper phthalocyanine nanoparticles with diameter between 3-5 nm. The TEM-SAED studies revealed the formation of 3-5 nm sized with beta-phase dominated mixture of alpha and beta copper phthalocyanine nanoparticles. The XRD, SEM, and the UV-vis studies were further carried out to confirm the formation of copper phthalocyanine thin films. The cyclic voltametry (CV) studies conclude that redox reaction is totally reversible one electron transfer process. The process is attributed to Cu(II)/Cu(I) redox reaction.

An approximate theoretical treatment of ion transfer processes at asymmetric microscopic and nanoscopic liquid-liquid interfaces: Single and double potential pulse techniques

NASA Astrophysics Data System (ADS)

Molina, A.; Laborda, E.; Compton, R. G.

2014-03-01

Simple theory for the electrochemical study of reversible ion transfer processes at micro- and nano-liquid|liquid interfaces supported on a capillary is presented. Closed-form expressions are obtained for the response in normal pulse and differential double pulse voltammetries, which describe adequately the particular behaviour of these systems due to the ‘asymmetric’ ion diffusion inside and outside the capillary. The use of different potential pulse techniques for the determination of the formal potential and diffusion coefficients of the ion is examined. For this, very simple analytical expressions are presented for the half-wave potential in NPV and the peak potential in DDPV.

CMCC Data Distribution Centre

NASA Astrophysics Data System (ADS)

Aloisio, Giovanni; Fiore, Sandro; Negro, A.

2010-05-01

The CMCC Data Distribution Centre (DDC) is the primary entry point (web gateway) to the CMCC. It is a Data Grid Portal providing a ubiquitous and pervasive way to ease data publishing, climate metadata search, datasets discovery, metadata annotation, data access, data aggregation, sub-setting, etc. The grid portal security model includes the use of HTTPS protocol for secure communication with the client (based on X509v3 certificates that must be loaded into the browser) and secure cookies to establish and maintain user sessions. The CMCC DDC is now in a pre-production phase and it is currently used only by internal users (CMCC researchers and climate scientists). The most important component already available in the CMCC DDC is the Search Engine which allows users to perform, through web interfaces, distributed search and discovery activities by introducing one or more of the following search criteria: horizontal extent (which can be specified by interacting with a geographic map), vertical extent, temporal extent, keywords, topics, creation date, etc. By means of this page the user submits the first step of the query process on the metadata DB, then, she can choose one or more datasets retrieving and displaying the complete XML metadata description (from the browser). This way, the second step of the query process is carried out by accessing to a specific XML document of the metadata DB. Finally, through the web interface, the user can access to and download (partially or totally) the data stored on the storage device accessing to OPeNDAP servers and to other available grid storage interfaces. Requests concerning datasets stored in deep storage will be served asynchronously.

The SOOS Data Portal, providing access to Southern Oceans data

NASA Astrophysics Data System (ADS)

Proctor, Roger; Finney, Kim; Blain, Peter; Taylor, Fiona; Newman, Louise; Meredith, Mike; Schofield, Oscar

2013-04-01

The Southern Ocean Observing System (SOOS) is an international initiative to enhance, coordinate and expand the strategic observations of the Southern Oceans that are required to address key scientific and societal challenges. A key component of SOOS will be the creation and maintenance of a Southern Ocean Data Portal to provide improved access to historical and ongoing data (Schofield et al., 2012, Eos, Vol. 93, No. 26, pp 241-243). The scale of this effort will require strong leveraging of existing data centres, new cyberinfrastructure development efforts, and defined data collection, quality control, and archiving procedures across the international community. The task of assembling the SOOS data portal is assigned to the SOOS Data Management Sub-Committee. The information infrastructure chosen for the SOOS data portal is based on the Australian Ocean Data Network (AODN, http://portal.aodn.org.au). The AODN infrastructure is built on open-source tools and the use of international standards ensures efficiency of data exchange and interoperability between contributing systems. OGC standard web services protocols are used for serving of data via the internet. These include Web Map Service (WMS) for visualisation, Web Feature Service (WFS) for data download, and Catalogue Service for Web (CSW) for catalogue exchange. The portal offers a number of tools to access and visualize data: - a Search link to the metadata catalogue enables search and discovery by simple text search, by geographic area, temporal extent, keyword, parameter, organisation, or by any combination of these, allowing users to gain access to further information and/or the data for download. Also, searches can be restricted to items which have either data to download, or attached map layers, or both - a Map interface for discovery and display of data, with the ability to change the style and opacity of layers, add additional data layers via OGC Web Map Services, view animated timeseries datastreams - data can be easily accessed and downloaded including directly from OPeNDAP/THREDDS servers. The SOOS data portal (http://soos.aodn.org.au/soos) aims to make access to Southern Ocean data a simple process and the initial layout classifies data into six themes - Heat and Freshwater; Circulation; Ice-sheets and Sea level; Carbon; Sea-ice; and Ecosystems, with the ability to integrate layers between themes. The portal is in its infancy (pilot launched January 2013) with a limited number of datasets available; however, the number of datasets is expected to grow rapidly as the international community becomes fully engaged.

Web Search Studies: Multidisciplinary Perspectives on Web Search Engines

NASA Astrophysics Data System (ADS)

Zimmer, Michael

Perhaps the most significant tool of our internet age is the web search engine, providing a powerful interface for accessing the vast amount of information available on the world wide web and beyond. While still in its infancy compared to the knowledge tools that precede it - such as the dictionary or encyclopedia - the impact of web search engines on society and culture has already received considerable attention from a variety of academic disciplines and perspectives. This article aims to organize a meta-discipline of “web search studies,” centered around a nucleus of major research on web search engines from five key perspectives: technical foundations and evaluations; transaction log analyses; user studies; political, ethical, and cultural critiques; and legal and policy analyses.

The Virtual Solar Observatory and the Heliophysics Meta-Virtual Observatory

NASA Technical Reports Server (NTRS)

Gurman, Joseph B.

2007-01-01

The Virtual Solar Observatory (VSO) is now able to search for solar data ranging from the radio to gamma rays, obtained from space and groundbased observatories, from 26 sources at 12 data providers, and from 1915 to the present. The solar physics community can use a Web interface or an Application Programming Interface (API) that allows integrating VSO searches into other software, including other Web services. Over the next few years, this integration will be especially obvious as the NASA Heliophysics division sponsors the development of a heliophysics-wide virtual observatory (VO), based on existing VO's in heliospheric, magnetospheric, and ionospheric physics as well as the VSO. We examine some of the challenges and potential of such a "meta-VO."

Design and usability study of an iconic user interface to ease information retrieval of medical guidelines.

PubMed

Griffon, Nicolas; Kerdelhué, Gaétan; Hamek, Saliha; Hassler, Sylvain; Boog, César; Lamy, Jean-Baptiste; Duclos, Catherine; Venot, Alain; Darmoni, Stéfan J

2014-10-01

Doc'CISMeF (DC) is a semantic search engine used to find resources in CISMeF-BP, a quality controlled health gateway, which gathers guidelines available on the internet in French. Visualization of Concepts in Medicine (VCM) is an iconic language that may ease information retrieval tasks. This study aimed to describe the creation and evaluation of an interface integrating VCM in DC in order to make this search engine much easier to use. Focus groups were organized to suggest ways to enhance information retrieval tasks using VCM in DC. A VCM interface was created and improved using the ergonomic evaluation approach. 20 physicians were recruited to compare the VCM interface with the non-VCM one. Each evaluator answered two different clinical scenarios in each interface. The ability and time taken to select a relevant resource were recorded and compared. A usability analysis was performed using the System Usability Scale (SUS). The VCM interface contains a filter based on icons, and icons describing each resource according to focus group recommendations. Some ergonomic issues were resolved before evaluation. Use of VCM significantly increased the success of information retrieval tasks (OR=11; 95% CI 1.4 to 507). Nonetheless, it took significantly more time to find a relevant resource with VCM interface (101 vs 65 s; p=0.02). SUS revealed 'good' usability with an average score of 74/100. VCM was successfully implemented in DC as an option. It increased the success rate of information retrieval tasks, despite requiring slightly more time, and was well accepted by end-users. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Category and Word Search: Generalizing Search Principles to Complex Processing.

DTIC Science & Technology

1982-03-01

complex processing (e.g., LaBerge & Samels, 1974; Shiffrin & Schneider, 1977). In the present paper we examine how well the major phenomena in simple visual...subjects are searching for novel characters ( LaBerge , 1973). The relatively large and rapid CH practice effects for word and category search are analogous...1974) demonstrated interference effects of irrelevant flanking letters. Shaffer and Laberge (1979) showed a similar effect with words and semantic

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.

The Auroral Planetary Imaging and Spectroscopy (APIS) service

NASA Astrophysics Data System (ADS)

Lamy, L.; Prangé, R.; Henry, F.; Le Sidaner, P.

2015-06-01

The Auroral Planetary Imaging and Spectroscopy (APIS) service, accessible online, provides an open and interactive access to processed auroral observations of the outer planets and their satellites. Such observations are of interest for a wide community at the interface between planetology, magnetospheric and heliospheric physics. APIS consists of (i) a high level database, built from planetary auroral observations acquired by the Hubble Space Telescope (HST) since 1997 with its mostly used Far-Ultraviolet spectro-imagers, (ii) a dedicated search interface aimed at browsing efficiently this database through relevant conditional search criteria and (iii) the ability to interactively work with the data online through plotting tools developed by the Virtual Observatory (VO) community, such as Aladin and Specview. This service is VO compliant and can therefore also been queried by external search tools of the VO community. The diversity of available data and the capability to sort them out by relevant physical criteria shall in particular facilitate statistical studies, on long-term scales and/or multi-instrumental multi-spectral combined analysis.

On the origin of the electrostatic potential difference at a liquid-vacuum interface.

PubMed

Harder, Edward; Roux, Benoît

2008-12-21

The microscopic origin of the interface potential calculated from computer simulations is elucidated by considering a simple model of molecules near an interface. The model posits that molecules are isotropically oriented and their charge density is Gaussian distributed. Molecules that have a charge density that is more negative toward their interior tend to give rise to a negative interface potential relative to the gaseous phase, while charge densities more positive toward their interior give rise to a positive interface potential. The interface potential for the model is compared to the interface potential computed from molecular dynamics simulations of the nonpolar vacuum-methane system and the polar vacuum-water interface system. The computed vacuum-methane interface potential from a molecular dynamics simulation (-220 mV) is captured with quantitative precision by the model. For the vacuum-water interface system, the model predicts a potential of -400 mV compared to -510 mV, calculated from a molecular dynamics simulation. The physical implications of this isotropic contribution to the interface potential is examined using the example of ion solvation in liquid methane.

SKITTER/implement mechanical interface

NASA Technical Reports Server (NTRS)

Cash, John Wilson, III; Cone, Alan E.; Garolera, Frank J.; German, David; Lindabury, David Peter; Luckado, Marshall Cleveland; Murphey, Craig; Rowell, John Bryan; Wilkinson, Brad

1988-01-01

SKITTER (Spacial Kinematic Inertial Translatory Tripod Extremity Robot) is a three-legged transport vehicle designed to perform under the unique environment of the moon. The objective of this project was to design a mechanical interface for SKITTER. This mechanical latching interface will allow SKITTER to use a series of implements such as drills, cranes, etc., and perform different tasks on the moon. The design emphasized versatility and detachability; that is, the interface design is the same for all implements, and connection and detachment is simple. After consideration of many alternatives, a system of three identical latches at each of the three interface points was chosen. The latching mechanism satisfies the design constraints because it facilitates connection and detachment. Also, the moving parts are protected from the dusty environment by housing plates.

Flexible Parsing.

DTIC Science & Technology

1986-06-30

Machine Studies .. 14. Minton, S. N., Hayes, P. J., and Fain, J. E. Controlling Search in Flexible Parsing. Proc. Ninth Int. Jt. Conf. on Artificial...interaction through the COUSIN command interface", International Journal of Man- Machine Studies , Vol. 19, No. 3, September 1983, pp. 285-305. 8...in a gracefully interacting user interface," "Dynamic strategy selection in flexible parsing," and "Parsing spoken language: a semantic case frame

Alternative Indices of Performance: An Exploration of Eye Gaze Metrics in a Visual Puzzle Task

DTIC Science & Technology

2014-07-01

strategy in which participants anchor their search on pieces in the correct positions results. Although there were significant effects for both...PERFORMANCE WING, HUMAN EFFECTIVENESS DIRECTORATE, WRIGHT-PATTERSON AIR FORCE BASE, OH 45433 AIR FORCE MATERIEL COMMAND UNITED STATES AIR FORCE...Interface Division //signed// WILLIAM E. RUSSELL Chief, Warfighter Interface Division Human Effectiveness Directorate 711 Human Performance

Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis.

PubMed

Cui, Licong; Xu, Rong; Luo, Zhihui; Wentz, Susan; Scarberry, Kyle; Zhang, Guo-Qiang

2014-08-03

Finding quality consumer health information online can effectively bring important public health benefits to the general population. It can empower people with timely and current knowledge for managing their health and promoting wellbeing. Despite a popular belief that search engines such as Google can solve all information access problems, recent studies show that using search engines and simple search terms is not sufficient. Our objective is to provide an approach to organizing consumer health information for navigational exploration, complementing keyword-based direct search. Multi-topic assignment to health information, such as online questions, is a fundamental step for navigational exploration. We introduce a new multi-topic assignment method combining semantic annotation using UMLS concepts (CUIs) and Formal Concept Analysis (FCA). Each question was tagged with CUIs identified by MetaMap. The CUIs were filtered with term-frequency and a new term-strength index to construct a CUI-question context. The CUI-question context and a topic-subject context were used for multi-topic assignment, resulting in a topic-question context. The topic-question context was then directly used for constructing a prototype navigational exploration interface. Experimental evaluation was performed on the task of automatic multi-topic assignment of 99 predefined topics for about 60,000 consumer health questions from NetWellness. Using example-based metrics, suitable for multi-topic assignment problems, our method achieved a precision of 0.849, recall of 0.774, and F₁ measure of 0.782, using a reference standard of 278 questions with manually assigned topics. Compared to NetWellness' original topic assignment, a 36.5% increase in recall is achieved with virtually no sacrifice in precision. Enhancing the recall of multi-topic assignment without sacrificing precision is a prerequisite for achieving the benefits of navigational exploration. Our new multi-topic assignment method, combining term-strength, FCA, and information retrieval techniques, significantly improved recall and performed well according to example-based metrics.

Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis

PubMed Central

2014-01-01

Background Finding quality consumer health information online can effectively bring important public health benefits to the general population. It can empower people with timely and current knowledge for managing their health and promoting wellbeing. Despite a popular belief that search engines such as Google can solve all information access problems, recent studies show that using search engines and simple search terms is not sufficient. Our objective is to provide an approach to organizing consumer health information for navigational exploration, complementing keyword-based direct search. Multi-topic assignment to health information, such as online questions, is a fundamental step for navigational exploration. Methods We introduce a new multi-topic assignment method combining semantic annotation using UMLS concepts (CUIs) and Formal Concept Analysis (FCA). Each question was tagged with CUIs identified by MetaMap. The CUIs were filtered with term-frequency and a new term-strength index to construct a CUI-question context. The CUI-question context and a topic-subject context were used for multi-topic assignment, resulting in a topic-question context. The topic-question context was then directly used for constructing a prototype navigational exploration interface. Results Experimental evaluation was performed on the task of automatic multi-topic assignment of 99 predefined topics for about 60,000 consumer health questions from NetWellness. Using example-based metrics, suitable for multi-topic assignment problems, our method achieved a precision of 0.849, recall of 0.774, and F1 measure of 0.782, using a reference standard of 278 questions with manually assigned topics. Compared to NetWellness’ original topic assignment, a 36.5% increase in recall is achieved with virtually no sacrifice in precision. Conclusion Enhancing the recall of multi-topic assignment without sacrificing precision is a prerequisite for achieving the benefits of navigational exploration. Our new multi-topic assignment method, combining term-strength, FCA, and information retrieval techniques, significantly improved recall and performed well according to example-based metrics. PMID:25086916

Determination of stress intensity factors for interface cracks under mixed-mode loading

NASA Technical Reports Server (NTRS)

Naik, Rajiv A.; Crews, John H., Jr.

1992-01-01

A simple technique was developed using conventional finite element analysis to determine stress intensity factors, K1 and K2, for interface cracks under mixed-mode loading. This technique involves the calculation of crack tip stresses using non-singular finite elements. These stresses are then combined and used in a linear regression procedure to calculate K1 and K2. The technique was demonstrated by calculating three different bimaterial combinations. For the normal loading case, the K's were within 2.6 percent of an exact solution. The normalized K's under shear loading were shown to be related to the normalized K's under normal loading. Based on these relations, a simple equation was derived for calculating K1 and K2 for mixed-mode loading from knowledge of the K's under normal loading. The equation was verified by computing the K's for a mixed-mode case with equal and normal shear loading. The correlation between exact and finite element solutions is within 3.7 percent. This study provides a simple procedure to compute K2/K1 ratio which has been used to characterize the stress state at the crack tip for various combinations of materials and loadings. Tests conducted over a range of K2/K1 ratios could be used to fully characterize interface fracture toughness.

Triple-loaded single-anchor stitch configurations: an analysis of cyclically loaded suture-tendon interface security.

PubMed

Coons, David A; Barber, F Alan; Herbert, Morley A

2006-11-01

This study evaluated the strength and suture-tendon interface security of different suture configurations from triple-suture-loaded anchors. A juvenile bovine infraspinatus tendon was detached and repaired by use of 4 different suture combinations from 2 suture anchors: 3 simple sutures in each anchor (ThreeVo anchor; Linvatec, Largo, FL); 2 peripheral simple stitches and 1 central horizontal mattress suture passed deeper into the tendon, creating a larger footprint (bigfoot-print anchor); 2 peripheral simple stitches with 1 central horizontal mattress stitch passed through the same holes as the simple sutures (stitch-of-Burns); and 2 simple stitches (TwoVo anchor; Linvatec). The constructs were cyclically loaded between 10 N and 180 N for 3,500 cycles and then destructively tested. The number of cycles required to create a 5-mm gap and a 10-mm gap and the ultimate load to failure and failure mode were recorded. The ThreeVo anchor was strongest and most resistant to cyclic loading (P < .01). The TwoVo anchor was least resistant to cyclic loading. The stitch-of-Burns anchor was more resistant to cyclic loading than both the bigfoot-print anchor and the TwoVo anchor (P < .03). The ThreeVo, stitch-of-Burns, and TwoVo anchors were stronger than the bigfoot-print anchor (P < .05). Three simple sutures in an anchor hold better than two simple sutures. Three simple sutures provide superior suture-tendon security than combinations of one mattress and two simple stitches subjected to cyclic loading. A central mattress stitch placed more medially than two peripheral simple stitches (bigfoot-print anchor) configured to enlarge the tendon-suture footprint was not as resistant to cyclic loading or destructive testing as three simple stitches (ThreeVo anchor). Placing a central mattress stitch more medially than 2 peripheral simple stitches to enlarge the tendon-suture footprint was not as resistant to cyclic loading or destructive testing as 3 simple stitches.

System for Performing Single Query Searches of Heterogeneous and Dispersed Databases

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Okimura, Takeshi (Inventor); Gurram, Mohana M. (Inventor); Tran, Vu Hoang (Inventor); Knight, Christopher D. (Inventor); Trinh, Anh Ngoc (Inventor)

2017-01-01

The present invention is a distributed computer system of heterogeneous databases joined in an information grid and configured with an Application Programming Interface hardware which includes a search engine component for performing user-structured queries on multiple heterogeneous databases in real time. This invention reduces overhead associated with the impedance mismatch that commonly occurs in heterogeneous database queries.

An Exploratory Study of School-Age Children's Use of a Heterogeneous Resource Site

ERIC Educational Resources Information Center

Holmes, Jason; Robins, David; Zhang, Yin; Salaba, Athena

2008-01-01

In this study, students' use of a new educational Web portal was evaluated with particular emphasis on searching and browsing strategies. The effects and implications of a federated search system are also discussed. Fifty-four students, ranging from 5th to 12th grade, were given five tasks to complete using the SchoolRooms interface. The tasks…

The User Interface of ERIC on the Macintosh: A Qualitative Study of Novice Users.

ERIC Educational Resources Information Center

Thomas, Patricia

The experience of novice users searching SilverPlatter's ERIC CD-ROM on the Macintosh was studied. Ten students from an introductory master's level course in library and information science were recruited as volunteer subjects. Subjects were asked to complete a search on the ERIC CD-ROM; and data were collected via observations, a think-aloud…

The Use of AJAX in Searching a Bibliographic Database: A Case Study of the Italian Biblioteche Oggi Database

ERIC Educational Resources Information Center

Cavaleri, Piero

2008-01-01

Purpose: The purpose of this paper is to describe the use of AJAX for searching the Biblioteche Oggi database of bibliographic records. Design/methodology/approach: The paper is a demonstration of how bibliographic database single page interfaces allow the implementation of more user-friendly features for social and collaborative tasks. Findings:…

RoLo: A Dictionary Interface that Minimizes Extraneous Cognitive Load of Lookup and Supports Incidental and Incremental Learning of Vocabulary

ERIC Educational Resources Information Center

Dang, Thanh-Dung; Chen, Gwo-Dong; Dang, Giao; Li, Liang-Yi; Nurkhamid

2013-01-01

Dictionary use can improve reading comprehension and incidental vocabulary learning. Nevertheless, great extraneous cognitive load imposed by the search process may reduce or even prevent the improvement. With the help of technology, dictionary users can now instantly access the meaning list of a searched word using a mouse click. However, they…

A collection of open source applications for mass spectrometry data mining.

PubMed

Gallardo, Óscar; Ovelleiro, David; Gay, Marina; Carrascal, Montserrat; Abian, Joaquin

2014-10-01

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An intuitive graphical webserver for multiple-choice protein sequence search.

PubMed

Banky, Daniel; Szalkai, Balazs; Grolmusz, Vince

2014-04-10

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at the given position. This computer-game-like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org. Copyright © 2014 Elsevier B.V. All rights reserved.

Approaching a flat boundary with a block copolymer coated emulsion drop: late stage drainage dynamics

NASA Astrophysics Data System (ADS)

Rozairo, Damith; Croll, Andrew

Understanding the dynamics of the formation and drainage of the thin fluid film that becomes trapped by a deformable droplet as it approaches another object is crucial to the advancement of many industrial and biomedical applications. Adding amphiphilic diblock copolymers, which are becoming more commonly used in drug delivery and oil recovery, only add to the complexity. Despite their increased use, little is known about how long polymer chains fill an emulsion drop's interface or how the molecules influence hydrodynamic processes. We study the drainage dynamics of a thin water film trapped between mica and a diblock copolymer saturated oil droplet. Specifically, we examine several different polystyrene-b-poly(ethylene oxide) (PS-PEO) molecules self-assembled at a toluene-water interface using laser scanning confocal microscopy. Our experiments reveal that the molecular details of the polymer chains deeply influence the drainage times, indicating that they are not acting as a 'simple' surfactant. The presence of the chains creates a much slower dynamic as fluid is forced to drain through an effective polymer brush, the brush itself determined by chain packing at the interface. We present a simple model which accounts for the basic physics of the interface.

The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex.

PubMed

Brzovic, Peter S; Heikaus, Clemens C; Kisselev, Leonid; Vernon, Robert; Herbig, Eric; Pacheco, Derek; Warfield, Linda; Littlefield, Peter; Baker, David; Klevit, Rachel E; Hahn, Steven

2011-12-23

The structural basis for binding of the acidic transcription activator Gcn4 and one activator-binding domain of the Mediator subunit Gal11/Med15 was examined by NMR. Gal11 activator-binding domain 1 has a four-helix fold with a small shallow hydrophobic cleft at its center. In the bound complex, eight residues of Gcn4 adopt a helical conformation, allowing three Gcn4 aromatic/aliphatic residues to insert into the Gal11 cleft. The protein-protein interface is dynamic and surprisingly simple, involving only hydrophobic interactions. This allows Gcn4 to bind Gal11 in multiple conformations and orientations, an example of a "fuzzy" complex, where the Gcn4-Gal11 interface cannot be described by a single conformation. Gcn4 uses a similar mechanism to bind two other unrelated activator-binding domains. Functional studies in yeast show the importance of residues at the protein interface, define the minimal requirements for a functional activator, and suggest a mechanism by which activators bind to multiple unrelated targets. Copyright © 2011 Elsevier Inc. All rights reserved.

A simple method for determining stress intensity factors for a crack in bi-material interface

NASA Astrophysics Data System (ADS)

Morioka, Yuta

Because of violently oscillating nature of stress and displacement fields near the crack tip, it is difficult to obtain stress intensity factors for a crack between two dis-similar media. For a crack in a homogeneous medium, it is a common practice to find stress intensity factors through strain energy release rates. However, individual strain energy release rates do not exist for bi-material interface crack. Hence it is necessary to find alternative methods to evaluate stress intensity factors. Several methods have been proposed in the past. However they involve mathematical complexity and sometimes require additional finite element analysis. The purpose of this research is to develop a simple method to find stress intensity factors in bi-material interface cracks. A finite element based projection method is proposed in the research. It is shown that the projection method yields very accurate stress intensity factors for a crack in isotropic and anisotropic bi-material interfaces. The projection method is also compared to displacement ratio method and energy method proposed by other authors. Through comparison it is found that projection method is much simpler to apply with its accuracy comparable to that of displacement ratio method.

The Chandra Source Catalog: Storage and Interfaces

NASA Astrophysics Data System (ADS)

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

2009-09-01

The Chandra Source Catalog (CSC) is part of the Chandra Data Archive (CDA) at the Chandra X-ray Center. The catalog contains source properties and associated data objects such as images, spectra, and lightcurves. The source properties are stored in relational databases and the data objects are stored in files with their metadata stored in databases. The CDA supports different versions of the catalog: multiple fixed release versions and a live database version. There are several interfaces to the catalog: CSCview, a graphical interface for building and submitting queries and for retrieving data objects; a command-line interface for property and source searches using ADQL; and VO-compliant services discoverable though the VO registry. This poster describes the structure of the catalog and provides an overview of the interfaces.

Have Users Changed Their Style? A Survey of CD-ROM vs. OPAC Product Usage.

ERIC Educational Resources Information Center

Anderson, Judy

1995-01-01

A survey of online search techniques of 50 undergraduate and graduate students at Arizona State University's Hayden Library revealed heavy reliance on simple subject searching. The analysis included search types, use of library personnel and online help screens, exposure to library instruction, and length of time at the terminal for citation…

Learning Problem-Solving Rules as Search through a Hypothesis Space

ERIC Educational Resources Information Center

Lee, Hee Seung; Betts, Shawn; Anderson, John R.

2016-01-01

Learning to solve a class of problems can be characterized as a search through a space of hypotheses about the rules for solving these problems. A series of four experiments studied how different learning conditions affected the search among hypotheses about the solution rule for a simple computational problem. Experiment 1 showed that a problem…

Pyrotechnic modeling for the NSI and pin puller

NASA Technical Reports Server (NTRS)

Powers, Joseph M.; Gonthier, Keith A.

1993-01-01

A discussion concerning the modeling of pyrotechnically driven actuators is presented in viewgraph format. The following topics are discussed: literature search, constitutive data for full-scale model, simple deterministic model, observed phenomena, and results from simple model.

Development of a Google-based search engine for data mining radiology reports.

PubMed

Erinjeri, Joseph P; Picus, Daniel; Prior, Fred W; Rubin, David A; Koppel, Paul

2009-08-01

The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google's XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like "pneumothorax" yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like "hemangioendothelioma" yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google's interface, radiologists can quickly perform useful searches.

Global search and rescue - A new concept. [orbital digital radar system with passive reflectors

NASA Technical Reports Server (NTRS)

Sivertson, W. E., Jr.

1976-01-01

A new terrestrial search and rescue concept is defined embodying the use of simple passive radiofreqeuncy reflectors in conjunction with a low earth-orbiting, all-weather, synthetic aperture radar to detect, identify, and position locate earth-bound users in distress. Users include ships, aircraft, small boats, explorers, hikers, etc. Airborne radar tests were conducted to evaluate the basic concept. Both X-band and L-band, dual polarization radars were operated simultaneously. Simple, relatively small, corner-reflector targets were successfully imaged and digital data processing approaches were investigated. Study of the basic concept and evaluation of results obtained from aircraft flight tests indicate an all-weather, day or night, global search and rescue system is feasible.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Designing an information search interface for younger and older adults.

PubMed

Pak, Richard; Price, Margaux M

2008-08-01

The present study examined Web-based information retrieval as a function of age for two information organization schemes: hierarchical organization and one organized around tags or keywords. Older adults' performance in information retrieval tasks has traditionally been lower compared with younger adults'. The current study examined the degree to which information organization moderated age-related performance differences on an information retrieval task. The theory of fluid and crystallized intelligence may provide insight into different kinds of information architectures that may reduce age-related differences in computer-based information retrieval performance. Fifty younger (18-23 years of age) and 50 older (55-76 years of age) participants browsed a Web site for answers to specific questions. Half of the participants browsed the hierarchically organized system (taxonomy), which maintained a one-to-one relationship between menu link and page, whereas the other half browsed the tag-based interface, with a many-to-one relationship between menu and page. This difference was expected to interact with age-related differences in fluid and crystallized intelligence. Age-related differences in information retrieval performance persisted; however, a tag-based retrieval interface reduced age-related differences, as compared with a taxonomical interface. Cognitive aging theory can lead to interface interventions that reduce age-related differences in performance with technology. In an information retrieval paradigm, older adults may be able to leverage their increased crystallized intelligence to offset fluid intelligence declines in a computer-based information search task. More research is necessary, but the results suggest that information retrieval interfaces organized around keywords may reduce age-related differences in performance.

A Web Application For Visualizing Empirical Models of the Space-Atmosphere Interface Region: AtModWeb

NASA Astrophysics Data System (ADS)

Knipp, D.; Kilcommons, L. M.; Damas, M. C.

2015-12-01

We have created a simple and user-friendly web application to visualize output from empirical atmospheric models that describe the lower atmosphere and the Space-Atmosphere Interface Region (SAIR). The Atmospheric Model Web Explorer (AtModWeb) is a lightweight, multi-user, Python-driven application which uses standard web technology (jQuery, HTML5, CSS3) to give an in-browser interface that can produce plots of modeled quantities such as temperature and individual species and total densities of neutral and ionized upper-atmosphere. Output may be displayed as: 1) a contour plot over a map projection, 2) a pseudo-color plot (heatmap) which allows visualization of a variable as a function of two spatial coordinates, or 3) a simple line plot of one spatial coordinate versus any number of desired model output variables. The application is designed around an abstraction of an empirical atmospheric model, essentially treating the model code as a black box, which makes it simple to add additional models without modifying the main body of the application. Currently implemented are the Naval Research Laboratory NRLMSISE00 model for neutral atmosphere and the International Reference Ionosphere (IRI). These models are relevant to the Low Earth Orbit environment and the SAIR. The interface is simple and usable, allowing users (students and experts) to specify time and location, and choose between historical (i.e. the values for the given date) or manual specification of whichever solar or geomagnetic activity drivers are required by the model. We present a number of use-case examples from research and education: 1) How does atmospheric density between the surface and 1000 km vary with time of day, season and solar cycle?; 2) How do ionospheric layers change with the solar cycle?; 3 How does the composition of the SAIR vary between day and night at a fixed altitude?

Adaptive mesh refinement techniques for the immersed interface method applied to flow problems

PubMed Central

Li, Zhilin; Song, Peng

2013-01-01

In this paper, we develop an adaptive mesh refinement strategy of the Immersed Interface Method for flow problems with a moving interface. The work is built on the AMR method developed for two-dimensional elliptic interface problems in the paper [12] (CiCP, 12(2012), 515–527). The interface is captured by the zero level set of a Lipschitz continuous function φ(x, y, t). Our adaptive mesh refinement is built within a small band of |φ(x, y, t)| ≤ δ with finer Cartesian meshes. The AMR-IIM is validated for Stokes and Navier-Stokes equations with exact solutions, moving interfaces driven by the surface tension, and classical bubble deformation problems. A new simple area preserving strategy is also proposed in this paper for the level set method. PMID:23794763

Control and Analysis for a Self-Excited Induction Generator for Wind Turbine and Electrolyzer Applications

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

Muljadi, Eduard; Na, Woonki; Leighty, Bill

Self-Excited Induction Generation(SEIG) is very rugged, simple, lightweight, and it is easy and inexpensive to implement, very simple to control, and requires a very little maintenance. In this variable-speed operation, the SEIG needs a power electronics interface to convert from the variable frequency output voltage of the generator to a DC output voltage for battery or other DC applications. In our study, a SEIG is connected to the power electronics interface such as diode rectifier and DC/DC converter and then an electrolyzer is connected as a final DC load for fuel cell applications. An equivalent circuit model for an electrolyzermore » is utilized for our application. The control and analysis for the proposed system is carried out by using PSCAD and MATLAB software. This study would be useful for designing and control analysis of power interface circuits for SEIG for a variable speed wind turbine generation with fuel cell applications before the actual implementation.« less

LIVIVO - the Vertical Search Engine for Life Sciences.

PubMed

Müller, Bernd; Poley, Christoph; Pössel, Jana; Hagelstein, Alexandra; Gübitz, Thomas

2017-01-01

The explosive growth of literature and data in the life sciences challenges researchers to keep track of current advancements in their disciplines. Novel approaches in the life science like the One Health paradigm require integrated methodologies in order to link and connect heterogeneous information from databases and literature resources. Current publications in the life sciences are increasingly characterized by the employment of trans-disciplinary methodologies comprising molecular and cell biology, genetics, genomic, epigenomic, transcriptional and proteomic high throughput technologies with data from humans, plants, and animals. The literature search engine LIVIVO empowers retrieval functionality by incorporating various literature resources from medicine, health, environment, agriculture and nutrition. LIVIVO is developed in-house by ZB MED - Information Centre for Life Sciences. It provides a user-friendly and usability-tested search interface with a corpus of 55 Million citations derived from 50 databases. Standardized application programming interfaces are available for data export and high throughput retrieval. The search functions allow for semantic retrieval with filtering options based on life science entities. The service oriented architecture of LIVIVO uses four different implementation layers to deliver search services. A Knowledge Environment is developed by ZB MED to deal with the heterogeneity of data as an integrative approach to model, store, and link semantic concepts within literature resources and databases. Future work will focus on the exploitation of life science ontologies and on the employment of NLP technologies in order to improve query expansion, filters in faceted search, and concept based relevancy rankings in LIVIVO.

FLASH Interface; a GUI for managing runtime parameters in FLASH simulations

NASA Astrophysics Data System (ADS)

Walker, Christopher; Tzeferacos, Petros; Weide, Klaus; Lamb, Donald; Flocke, Norbert; Feister, Scott

2017-10-01

We present FLASH Interface, a novel graphical user interface (GUI) for managing runtime parameters in simulations performed with the FLASH code. FLASH Interface supports full text search of available parameters; provides descriptions of each parameter's role and function; allows for the filtering of parameters based on categories; performs input validation; and maintains all comments and non-parameter information already present in existing parameter files. The GUI can be used to edit existing parameter files or generate new ones. FLASH Interface is open source and was implemented with the Electron framework, making it available on Mac OSX, Windows, and Linux operating systems. The new interface lowers the entry barrier for new FLASH users and provides an easy-to-use tool for experienced FLASH simulators. U.S. Department of Energy (DOE), NNSA ASC/Alliances Center for Astrophysical Thermonuclear Flashes, U.S. DOE NNSA ASC through the Argonne Institute for Computing in Science, U.S. National Science Foundation.

A Standardized Interface for Obtaining Digital Planetary and Heliophysics Time Series Data

NASA Astrophysics Data System (ADS)

Vandegriff, Jon; Weigel, Robert; Faden, Jeremy; King, Todd; Candey, Robert

2016-10-01

We describe a low level interface for accessing digital Planetary and Heliophysics data, focusing primarily on time-series data from in-situ instruments. As the volume and variety of planetary data has increased, it has become harder to merge diverse datasets into a common analysis environment. Thus we are building low-level computer-to-computer infrastructure to enable data from different missions or archives to be able to interoperate. The key to enabling interoperability is a simple access interface that standardizes the common capabilities available from any data server: 1. identify the data resources that can be accessed; 2. describe each resource; and 3. get the data from a resource. We have created a standardized way for data servers to perform each of these three activities. We are also developing a standard streaming data format for the actual data content to be returned (i.e., the result of item 3). Our proposed standard access interface is simple enough that it could be implemented on top of or beside existing data services, or it could even be fully implemented by a small data provider as a way to ensure that the provider's holdings can participate in larger data systems or joint analysis with other datasets. We present details of the interface and of the streaming format, including a sample server designed to illustrate the data request and streaming capabilities.

The One Universal Graph — a free and open graph database

NASA Astrophysics Data System (ADS)

Ng, Liang S.; Champion, Corbin

2016-02-01

Recent developments in graph database mostly are huge projects involving big organizations, big operations and big capital, as the name Big Data attests. We proposed the concept of One Universal Graph (OUG) which states that all observable and known objects and concepts (physical, conceptual or digitally represented) can be connected with only one single graph; furthermore the OUG can be implemented with a very simple text file format with free software, capable of being executed on Android or smaller devices. As such the One Universal Graph Data Exchange (GOUDEX) modules can potentially be installed on hundreds of millions of Android devices and Intel compatible computers shipped annually. Coupled with its open nature and ability to connect to existing leading search engines and databases currently in operation, GOUDEX has the potential to become the largest and a better interface for users and programmers to interact with the data on the Internet. With a Web User Interface for users to use and program in native Linux environment, Free Crowdware implemented in GOUDEX can help inexperienced users learn programming with better organized documentation for free software, and is able to manage programmer's contribution down to a single line of code or a single variable in software projects. It can become the first practically realizable “Internet brain” on which a global artificial intelligence system can be implemented. Being practically free and open, One Universal Graph can have significant applications in robotics, artificial intelligence as well as social networks.

Hands-On TAROT: Intercontinental Use of the TAROT for Education and Public Outreach

NASA Astrophysics Data System (ADS)

Boër, M.; Thiébaut, C.; Klotz, A.; Buchholtz, G.; Melchior, A.-L.; Pennypaker, C.; Isaac, M.; Ebisuzaki, T.

The TAROT telescope has for primary goal the search for the prompt optical counterpart of cosmic Gamma-Ray Bursts. It is a completely autonomous 25cm telescope installed near Nice (France), able to point to any location of the sky within 1-2 seconds. The control, scheduling, and data processing activities are completely automated. In addition to its un-manned modes, we added recently the possibility to control the telescope remotely, as a request of the ``Hands-On Universe'' (HOU) program of using automatic telescopes for education and public outreach. To this purpose we developed a simple control interface. A webcam was installed to visualize the telescope. Access to the data is possible through a web interface. The images can be processed by the HOU software, a program specially suited for use within the classroom. We used these feature during the open days of the University of California Berkeley and the Astronomy Festival of Fleurance (France). We plan regular use for an astronomy course of the Museum of Tokyo, as well as for French schools. Not only does Hands-On TAROT gives the general public access to professional astronomy, it is also a more general tool to demonstrate the use of a complex automated system, the techniques of data processing and automation. Last but not least, through the use of telescopes located in many countries over the globe, a powerful and genuine cooperation between teachers and children from various countries is promoted, with a clear educational goal.

EST-PAC a web package for EST annotation and protein sequence prediction

PubMed Central

Strahm, Yvan; Powell, David; Lefèvre, Christophe

2006-01-01

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics. PMID:17147782

Automatic document classification of biological literature

PubMed Central

Chen, David; Müller, Hans-Michael; Sternberg, Paul W

2006-01-01

Background Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusion We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. PMID:16893465

PepArML: A Meta-Search Peptide Identification Platform

PubMed Central

Edwards, Nathan J.

2014-01-01

The PepArML meta-search peptide identification platform provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score, and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores — reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies 2–3 times more spectra than individual search engines at 10% FDR. PMID:25663956

Differential recall of derived and inflected word forms in working memory: examining the role of morphological information in simple and complex working memory tasks

PubMed Central

Service, Elisabet; Maury, Sini

2015-01-01

Working memory (WM) has been described as an interface between cognition and action, or a system for access to a limited amount of information needed in complex cognition. Access to morphological information is needed for comprehending and producing sentences. The present study probed WM for morphologically complex word forms in Finnish, a morphologically rich language. We studied monomorphemic (boy), inflected (boy+’s), and derived (boy+hood) words in three tasks. Simple span, immediate serial recall of words, in Experiment 1, is assumed to mainly rely on information in the focus of attention. Sentence span, a dual task combining sentence reading with recall of the last word (Experiment 2) or of a word not included in the sentence (Experiment 3) is assumed to involve establishment of a search set in long-term memory for fast activation into the focus of attention. Recall was best for monomorphemic and worst for inflected word forms with performance on derived words in between. However, there was an interaction between word type and experiment, suggesting that complex span is more sensitive to morphological complexity in derivations than simple span. This was explored in a within-subjects Experiment 4 combining all three tasks. An interaction between morphological complexity and task was replicated. Both inflected and derived forms increased load in WM. In simple span, recall of inflectional forms resulted in form errors. Complex span tasks were more sensitive to morphological load in derived words, possibly resulting from interference from morphological neighbors in the mental lexicon. The results are best understood as involving competition among inflectional forms when binding words from input into an output structure, and competition from morphological neighbors in secondary memory during cumulative retrieval-encoding cycles. Models of verbal recall need to be able to represent morphological as well as phonological and semantic information. PMID:25642181

Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms.

PubMed

Kim, Sun; Yeganova, Lana; Wilbur, W John

2016-10-01

Medical Subject Headings (MeSH(®)) is a controlled vocabulary for indexing and searching biomedical literature. MeSH terms and subheadings are organized in a hierarchical structure and are used to indicate the topics of an article. Biologists can use either MeSH terms as queries or the MeSH interface provided in PubMed(®) for searching PubMed abstracts. However, these are rarely used, and there is no convenient way to link standardized MeSH terms to user queries. Here, we introduce a web interface which allows users to enter queries to find MeSH terms closely related to the queries. Our method relies on co-occurrence of text words and MeSH terms to find keywords that are related to each MeSH term. A query is then matched with the keywords for MeSH terms, and candidate MeSH terms are ranked based on their relatedness to the query. The experimental results show that our method achieves the best performance among several term extraction approaches in terms of topic coherence. Moreover, the interface can be effectively used to find full names of abbreviations and to disambiguate user queries. https://www.ncbi.nlm.nih.gov/IRET/MESHABLE/ CONTACT: sun.kim@nih.gov Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

What Do We Really Need? Visions of an Ideal Human-Machine Interface for NOTES Mechatronic Support Systems From the View of Surgeons, Gastroenterologists, and Medical Engineers.

PubMed

Kranzfelder, Michael; Schneider, Armin; Fiolka, Adam; Koller, Sebastian; Wilhelm, Dirk; Reiser, Silvano; Meining, Alexander; Feussner, Hubertus

2015-08-01

To investigate why natural orifice translumenal endoscopic surgery (NOTES) has not yet become widely accepted and to prove whether the main reason is still the lack of appropriate platforms due to the deficiency of applicable interfaces. To assess expectations of a suitable interface design, we performed a survey on human-machine interfaces for NOTES mechatronic support systems among surgeons, gastroenterologists, and medical engineers. Of 120 distributed questionnaires, each consisting of 14 distinct questions, 100 (83%) were eligible for analysis. A mechatronic platform for NOTES was considered "important" by 71% of surgeons, 83% of gastroenterologist,s and 56% of medical engineers. "Intuitivity" and "simple to use" were the most favored aspects (33% to 51%). Haptic feedback was considered "important" by 70% of participants. In all, 53% of surgeons, 50% of gastroenterologists, and 33% of medical engineers already had experience with NOTES platforms or other surgical robots; however, current interfaces only met expectations in just more than 50%. Whereas surgeons did not favor a certain working posture, gastroenterologists and medical engineers preferred a sitting position. Three-dimensional visualization was generally considered "nice to have" (67% to 72%); however, for 26% of surgeons, 17% of gastroenterologists, and 7% of medical engineers it did not matter (P = 0.018). Requests and expectations of human-machine interfaces for NOTES seem to be generally similar for surgeons, gastroenterologist, and medical engineers. Consensus exists on the importance of developing interfaces that should be both intuitive and simple to use, are similar to preexisting familiar instruments, and exceed current available systems. © The Author(s) 2014.

Improving PHENIX search with Solr, Nutch and Drupal.

NASA Astrophysics Data System (ADS)

Morrison, Dave; Sourikova, Irina

2012-12-01

During its 20 years of R&D, construction and operation the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC) has accumulated large amounts of proprietary collaboration data that is hosted on many servers around the world and is not open for commercial search engines for indexing and searching. The legacy search infrastructure did not scale well with the fast growing PHENIX document base and produced results inadequate in both precision and recall. After considering the possible alternatives that would provide an aggregated, fast, full text search of a variety of data sources and file formats we decided to use Nutch [1] as a web crawler and Solr [2] as a search engine. To present XML-based Solr search results in a user-friendly format we use Drupal [3] as a web interface to Solr. We describe the experience of building a federated search for a heterogeneous collection of 10 million PHENIX documents with Nutch, Solr and Drupal.

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.

Towards a Warfighter’s Associate: Eliminating the Operator Control Unit

DTIC Science & Technology

2004-10-01

ABSTRACT This paper introduces the long-term concept of a supervised autonomous Warfighter’s Associate, which uses a natural-language interface for...paper introduces the long-term concept of a supervised autonomous Warfighter’s Associate, which employs a natural-language interface for communication...results to date. The primary application discussed is military, but the concept also applies to law enforcement, space exploration, and search-and

Earthdata 3.0: A Unified Experience and Platform for Earth Science Discovery

NASA Astrophysics Data System (ADS)

Plofchan, P.; McLaughlin, B. D.

2015-12-01

NASA's EOSDIS (Earth Observing System Data and Information System) as a multitude of websites and applications focused on serving the Earth Science community's extensive data needs. With no central user interface, theme, or mechanism for accessing that data, interrelated systems are confusing and potentially disruptive in users' searches for EOSDIS data holdings. In an effort to bring consistency across these systems, an effort was undertaken to develop Earthdata 3.0: a complete information architecture overhaul of the Earthdata website, a significant update to the Earthdata user experience and user interface, and an increased focus on searching across EOSDIS data holdings, including those housed and made available through DAAC websites. As part of this effort, and in a desire to unify the user experience across related websites, the Earthdata User Interface (EUI) was developed. The EUI is a collection of responsive design components and layouts geared toward creating websites and applications within the Earthdata ecosystem. Each component and layout has been designed specifically for Earth science-related projects which eliminates some of the complexities of building a website or application from the ground up. Its adoption will ensure both consistent markup and a unified look and feel for end users, thereby increasing usability and accessibility. Additionally, through the user of a Google Search Appliance, custom Clojure code, and in cooperation with DAACs, Earthdata 3.0 presents a variety of search results upon a user's keyword(s) entry. These results are not just textual links, but also direct links to downloadable datasets, visualizations of datasets and collections of data, and related articles and videos for further research. The end result of the development of the EUI and the enhanced multi-response type search is a consistent and usable platform for Earth scientists and users to navigate and locate data to further their research.

Patterning nanoparticles into rings by "2-D Pickering emulsions".

PubMed

Lee, Cheol Hee; Crosby, Alfred J; Hayward, Ryan C; Emrick, Todd

2014-04-09

We present a simple method for the two-dimensional self-assembly of CdSe/ZnS quantum dots (QDs) into well-defined rings at the air/water interface, through the formation of "2-D Pickering emulsions". Surfactant molecules assemble at the air/water interface into islands that are subsequently surrounded by adsorption of QDs from the aqueous subphase. The QD rings emanating from this process range from ∼100 nm to several micrometers in diameter, as characterized by atomic force microscopy, scanning electron microscopy, and fluorescence microscopy. The deposition and alignment of QD rings onto large areas (cm(2)) were demonstrated by dip-coating onto a substrate. This simple method produces rings of QDs without the need for any templating or fabrication steps.

Things Forgotten: Simple Lapse or Serious Problem?

MedlinePlus

... part of the U.S. Department of Health and Human Services Search form Search ... went there. And misplaced your keys or eyeglasses at least a few times. Many people worry about these memory lapses. They fear they’re heading toward a ...

Plug Your Users into Library Resources with OpenSearch Plug-Ins

ERIC Educational Resources Information Center

Baker, Nicholas C.

2007-01-01

To bring the library catalog and other online resources right into users' workspace quickly and easily without needing much more than a short XML file, the author, a reference and Web services librarian at Williams College, learned to build and use OpenSearch plug-ins. OpenSearch is a set of simple technologies and standards that allows the…

Real-time scheduling using minimum search

NASA Technical Reports Server (NTRS)

Tadepalli, Prasad; Joshi, Varad

1992-01-01

In this paper we consider a simple model of real-time scheduling. We present a real-time scheduling system called RTS which is based on Korf's Minimin algorithm. Experimental results show that the schedule quality initially improves with the amount of look-ahead search and tapers off quickly. So it sppears that reasonably good schedules can be produced with a relatively shallow search.

Searching for light dark matter with the SLAC millicharge experiment.

PubMed

Diamond, M; Schuster, P

2013-11-27

New sub-GeV gauge forces ("dark photons") that kinetically mix with the photon provide a promising scenario for MeV-GeV dark matter and are the subject of a program of searches at fixed-target and collider facilities around the world. In such models, dark photons produced in collisions may decay invisibly into dark-matter states, thereby evading current searches. We reexamine results of the SLAC mQ electron beam dump experiment designed to search for millicharged particles and find that it was strongly sensitive to any secondary beam of dark matter produced by electron-nucleus collisions in the target. The constraints are competitive for dark photon masses in the ~1-30 MeV range, covering part of the parameter space that can reconcile the apparent (g-2)(μ) anomaly. Simple adjustments to the original SLAC search for millicharges may extend sensitivity to cover a sizable portion of the remaining (g-2)(μ) anomaly-motivated region. The mQ sensitivity is therefore complementary to ongoing searches for visible decays of dark photons. Compared to existing direct-detection searches, mQ sensitivity to electron-dark-matter scattering cross sections is more than an order of magnitude better for a significant range of masses and couplings in simple models.

Chips: A Tool for Developing Software Interfaces Interactively.

DTIC Science & Technology

1987-10-01

of the application through the objects on the screen. Chips makes this easy by supplying simple and direct access to the source code and data ...object-oriented programming, user interface management systems, programming environments. Typographic Conventions Technical terms appearing in the...creating an environment in which we could do our work. This project could not have happened without him. Jeff Bonar started and managed the Chips

Snap-in of particles at curved liquid interfaces

NASA Astrophysics Data System (ADS)

Li, Chao; Moradiafrapoli, Momene; Marston, Jeremy

2016-11-01

The contact of particles with liquid interfaces constitutes the first stage in the formation of a particle-laden interface, the so-called "snap-in effect". Here, we report on an experimental study using high-speed video to directly visualize the snap-in process and the approach to the equilibrium state of a particle at a curved liquid interface (i.e. droplet surface). We image the evolution of the contact line, which is found to follow a power-law scaling in time, and the dynamic contact angle during the snap-in. Both hydrophilic and hydrophobic particles are explored and we match the lift-off stage of the particles with a simple force balance. We also explore some multi-particle experiments, eluding to the dynamics of particle-laden interface formation.

Applying Spatial Audio to Human Interfaces: 25 Years of NASA Experience

NASA Technical Reports Server (NTRS)

Begault, Durand R.; Wenzel, Elizabeth M.; Godfrey, Martine; Miller, Joel D.; Anderson, Mark R.

2010-01-01

From the perspective of human factors engineering, the inclusion of spatial audio within a human-machine interface is advantageous from several perspectives. Demonstrated benefits include the ability to monitor multiple streams of speech and non-speech warning tones using a cocktail party advantage, and for aurally-guided visual search. Other potential benefits include the spatial coordination and interaction of multimodal events, and evaluation of new communication technologies and alerting systems using virtual simulation. Many of these technologies were developed at NASA Ames Research Center, beginning in 1985. This paper reviews examples and describes the advantages of spatial sound in NASA-related technologies, including space operations, aeronautics, and search and rescue. The work has involved hardware and software development as well as basic and applied research.

Natural interaction for unmanned systems

NASA Astrophysics Data System (ADS)

Taylor, Glenn; Purman, Ben; Schermerhorn, Paul; Garcia-Sampedro, Guillermo; Lanting, Matt; Quist, Michael; Kawatsu, Chris

2015-05-01

Military unmanned systems today are typically controlled by two methods: tele-operation or menu-based, search-andclick interfaces. Both approaches require the operator's constant vigilance: tele-operation requires constant input to drive the vehicle inch by inch; a menu-based interface requires eyes on the screen in order to search through alternatives and select the right menu item. In both cases, operators spend most of their time and attention driving and minding the unmanned systems rather than on being a warfighter. With these approaches, the platform and interface become more of a burden than a benefit. The availability of inexpensive sensor systems in products such as Microsoft Kinect™ or Nintendo Wii™ has resulted in new ways of interacting with computing systems, but new sensors alone are not enough. Developing useful and usable human-system interfaces requires understanding users and interaction in context: not just what new sensors afford in terms of interaction, but how users want to interact with these systems, for what purpose, and how sensors might enable those interactions. Additionally, the system needs to reliably make sense of the user's inputs in context, translate that interpretation into commands for the unmanned system, and give feedback to the user. In this paper, we describe an example natural interface for unmanned systems, called the Smart Interaction Device (SID), which enables natural two-way interaction with unmanned systems including the use of speech, sketch, and gestures. We present a few example applications SID to different types of unmanned systems and different kinds of interactions.

Remote Control and Data Acquisition: A Case Study

NASA Technical Reports Server (NTRS)

DeGennaro, Alfred J.; Wilkinson, R. Allen

2000-01-01

This paper details software tools developed to remotely command experimental apparatus, and to acquire and visualize the associated data in soft real time. The work was undertaken because commercial products failed to meet the needs. This work has identified six key factors intrinsic to development of quality research laboratory software. Capabilities include access to all new instrument functions without any programming or dependence on others to write drivers or virtual instruments, simple full screen text-based experiment configuration and control user interface, months of continuous experiment run-times, order of 1% CPU load for condensed matter physics experiment described here, very little imposition of software tool choices on remote users, and total remote control from anywhere in the world over the Internet or from home on a 56 Kb modem as if the user is sitting in the laboratory. This work yielded a set of simple robust tools that are highly reliable, resource conserving, extensible, and versatile, with a uniform simple interface.

Named Entity Recognition in a Hungarian NL Based QA System

NASA Astrophysics Data System (ADS)

Tikkl, Domonkos; Szidarovszky, P. Ferenc; Kardkovacs, Zsolt T.; Magyar, Gábor

In WoW project our purpose is to create a complex search interface with the following features: search in the deep web content of contracted partners' databases, processing Hungarian natural language (NL) questions and transforming them to SQL queries for database access, image search supported by a visual thesaurus that describes in a structural form the visual content of images (also in Hungarian). This paper primarily focuses on a particular problem of question processing task: the entity recognition. Before going into details we give a short overview of the project's aims.

Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation

NASA Astrophysics Data System (ADS)

Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.

2012-02-01

In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.

User needs analysis and usability assessment of DataMed - a biomedical data discovery index.

PubMed

Dixit, Ram; Rogith, Deevakar; Narayana, Vidya; Salimi, Mandana; Gururaj, Anupama; Ohno-Machado, Lucila; Xu, Hua; Johnson, Todd R

2017-11-30

To present user needs and usability evaluations of DataMed, a Data Discovery Index (DDI) that allows searching for biomedical data from multiple sources. We conducted 2 phases of user studies. Phase 1 was a user needs analysis conducted before the development of DataMed, consisting of interviews with researchers. Phase 2 involved iterative usability evaluations of DataMed prototypes. We analyzed data qualitatively to document researchers' information and user interface needs. Biomedical researchers' information needs in data discovery are complex, multidimensional, and shaped by their context, domain knowledge, and technical experience. User needs analyses validate the need for a DDI, while usability evaluations of DataMed show that even though aggregating metadata into a common search engine and applying traditional information retrieval tools are promising first steps, there remain challenges for DataMed due to incomplete metadata and the complexity of data discovery. Biomedical data poses distinct problems for search when compared to websites or publications. Making data available is not enough to facilitate biomedical data discovery: new retrieval techniques and user interfaces are necessary for dataset exploration. Consistent, complete, and high-quality metadata are vital to enable this process. While available data and researchers' information needs are complex and heterogeneous, a successful DDI must meet those needs and fit into the processes of biomedical researchers. Research directions include formalizing researchers' information needs, standardizing overviews of data to facilitate relevance judgments, implementing user interfaces for concept-based searching, and developing evaluation methods for open-ended discovery systems such as DDIs. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.

PubMed

de Andrade, Roberto R S; Vaslin, Maite F S

2014-03-07

Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

PubMed Central

2014-01-01

Background Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. Methods In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. Results The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. Conclusions SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. Availability and implementation SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/. PMID:24607237

Search efficiency of biased migration towards stationary or moving targets in heterogeneously structured environments

NASA Astrophysics Data System (ADS)

Azimzade, Youness; Mashaghi, Alireza

2017-12-01

Efficient search acts as a strong selective force in biological systems ranging from cellular populations to predator-prey systems. The search processes commonly involve finding a stationary or mobile target within a heterogeneously structured environment where obstacles limit migration. An open generic question is whether random or directionally biased motions or a combination of both provide an optimal search efficiency and how that depends on the motility and density of targets and obstacles. To address this question, we develop a simple model that involves a random walker searching for its targets in a heterogeneous medium of bond percolation square lattice and used mean first passage time (〈T 〉 ) as an indication of average search time. Our analysis reveals a dual effect of directional bias on the minimum value of 〈T 〉 . For a homogeneous medium, directionality always decreases 〈T 〉 and a pure directional migration (a ballistic motion) serves as the optimized strategy, while for a heterogeneous environment, we find that the optimized strategy involves a combination of directed and random migrations. The relative contribution of these modes is determined by the density of obstacles and motility of targets. Existence of randomness and motility of targets add to the efficiency of search. Our study reveals generic and simple rules that govern search efficiency. Our findings might find application in a number of areas including immunology, cell biology, ecology, and robotics.

Interface design and human factors considerations for model-based tight glycemic control in critical care.

PubMed

Ward, Logan; Steel, James; Le Compte, Aaron; Evans, Alicia; Tan, Chia-Siong; Penning, Sophie; Shaw, Geoffrey M; Desaive, Thomas; Chase, J Geoffrey

2012-01-01

Tight glycemic control (TGC) has shown benefits but has been difficult to implement. Model-based methods and computerized protocols offer the opportunity to improve TGC quality and compliance. This research presents an interface design to maximize compliance, minimize real and perceived clinical effort, and minimize error based on simple human factors and end user input. The graphical user interface (GUI) design is presented by construction based on a series of simple, short design criteria based on fundamental human factors engineering and includes the use of user feedback and focus groups comprising nursing staff at Christchurch Hospital. The overall design maximizes ease of use and minimizes (unnecessary) interaction and use. It is coupled to a protocol that allows nurse staff to select measurement intervals and thus self-manage workload. The overall GUI design is presented and requires only one data entry point per intervention cycle. The design and main interface are heavily focused on the nurse end users who are the predominant users, while additional detailed and longitudinal data, which are of interest to doctors guiding overall patient care, are available via tabs. This dichotomy of needs and interests based on the end user's immediate focus and goals shows how interfaces must adapt to offer different information to multiple types of users. The interface is designed to minimize real and perceived clinical effort, and ongoing pilot trials have reported high levels of acceptance. The overall design principles, approach, and testing methods are based on fundamental human factors principles designed to reduce user effort and error and are readily generalizable. © 2012 Diabetes Technology Society.

Interface Design and Human Factors Considerations for Model-Based Tight Glycemic Control in Critical Care

PubMed Central

Ward, Logan; Steel, James; Le Compte, Aaron; Evans, Alicia; Tan, Chia-Siong; Penning, Sophie; Shaw, Geoffrey M; Desaive, Thomas; Chase, J Geoffrey

2012-01-01

Introduction Tight glycemic control (TGC) has shown benefits but has been difficult to implement. Model-based methods and computerized protocols offer the opportunity to improve TGC quality and compliance. This research presents an interface design to maximize compliance, minimize real and perceived clinical effort, and minimize error based on simple human factors and end user input. Method The graphical user interface (GUI) design is presented by construction based on a series of simple, short design criteria based on fundamental human factors engineering and includes the use of user feedback and focus groups comprising nursing staff at Christchurch Hospital. The overall design maximizes ease of use and minimizes (unnecessary) interaction and use. It is coupled to a protocol that allows nurse staff to select measurement intervals and thus self-manage workload. Results The overall GUI design is presented and requires only one data entry point per intervention cycle. The design and main interface are heavily focused on the nurse end users who are the predominant users, while additional detailed and longitudinal data, which are of interest to doctors guiding overall patient care, are available via tabs. This dichotomy of needs and interests based on the end user's immediate focus and goals shows how interfaces must adapt to offer different information to multiple types of users. Conclusions The interface is designed to minimize real and perceived clinical effort, and ongoing pilot trials have reported high levels of acceptance. The overall design principles, approach, and testing methods are based on fundamental human factors principles designed to reduce user effort and error and are readily generalizable. PMID:22401330

Structure and functions of simple membrane-water interfaces. [Abstract only

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M. A.

1994-01-01

The structure and functions of the earliest ancestors of contemporary cells are focal points in studies of the origin of life. Probably the first cell-like structures were vesicles - closed, spheroidal structures with aqueous medium trapped inside. The membranous walls of vesicles were most likely bilayers composed of simple amphiphilic material available on early earth. The membrane studied was composed of glycerol 1-monooleate (GMO). Glycerol forms the polar head group and the oily tail contains 18 carbon atoms. All head groups have been found to be located in two narrow regions at the interfaces with water. The membrane interior, formed by the hydrophobic tails, is quite fluid with chain disorder increasing towards the center of the bilayer. These results are in agreement with x-ray and neutron scattering data from related bilayers. The width of the membrane is not constant, but fluctuates in time and space. Occasional thinning defects in the membrane, observed during the course of the simulations, may have a significant influence on rates of passive transport of small molecules across membranes. It has been found that water penetrates the head group region but not the oily interior of the membrane. Water molecules near the interface are oriented by dipoles of the head groups. The resulting electrostatic potential across the interface, determined in our simulations, has been found to be markedly larger than across the water-oil interface. This quantity has been implicated as the source of selectivity, with respect to the sign of the charge, as an ion approaches the interface and during transport of hydrophobic ions across membranes.

Molecular discriminators using single wall carbon nanotubes

NASA Astrophysics Data System (ADS)

Bhattacharyya, Tamoghna; Dasgupta, Anjan Kr; Ranjan Ray, Nihar; Sarkar, Sabyasachi

2012-09-01

The interaction between single wall carbon nanotubes (SWNTs) and amphiphilic molecules has been studied in a solid phase. SWNTs are allowed to interact with different amphiphilic probes (e.g. lipids) in a narrow capillary interface. Contact between strong hydrophobic and amphiphilic interfaces leads to a molecular restructuring of the lipids at the interface. The geometry of the diffusion front and the rate and the extent of diffusion of the interface are dependent on the structure of the lipid at the interface. Lecithin having a linear tail showed greater mobility of the interface as compared to a branched tail lipid like dipalmitoyl phosphatidylcholine, indicating the hydrophobic interaction between single wall carbon nanotube core and the hydrophobic tail of the lipid. Solid phase interactions between SWNT and lipids can thus become a very simple but efficient means of discriminating amphiphilic molecules in general and lipids in particular.

A four-port vertical-coupling optical interface based on two-dimensional grating coupler

NASA Astrophysics Data System (ADS)

Zhang, Zan; Zhang, Zanyun; Huang, Beiju; Cheng, Chuantong; Gao, Tianxi; Hu, Xiaochuan; Zhang, Lin; Chen, Hongda

2016-10-01

In this work, a fiber-to-chip optical interface with four output ports is proposed. External lights irradiate vertically from single mode fiber to the center of optical interface can be coupled into silicon photonic chips and split into four siliconon- insulator (SOI) waveguides. If the light is circular polarized, the power of light will be equally split into four ports. Meanwhile, all lights travel in the four channel will be converted into TE polarization. The optical interface is based on a two-dimensional grating coupler with carefully designed duty cycle and period. Simulation results show that the coupling efficiency of each port can reach 11.6% so that the total coupling efficiency of the interface is 46.4%. And Lights coupled into four waveguides are all converted into TE polarization. Further, the optical interface has a simple grating structure allowing for easy fabrication.

Gestures in an Intelligent User Interface

NASA Astrophysics Data System (ADS)

Fikkert, Wim; van der Vet, Paul; Nijholt, Anton

In this chapter we investigated which hand gestures are intuitive to control a large display multimedia interface from a user's perspective. Over the course of two sequential user evaluations, we defined a simple gesture set that allows users to fully control a large display multimedia interface, intuitively. First, we evaluated numerous gesture possibilities for a set of commands that can be issued to the interface. These gestures were selected from literature, science fiction movies, and a previous exploratory study. Second, we implemented a working prototype with which the users could interact with both hands and the preferred hand gestures with 2D and 3D visualizations of biochemical structures. We found that the gestures are influenced to significant extent by the fast paced developments in multimedia interfaces such as the Apple iPhone and the Nintendo Wii and to no lesser degree by decades of experience with the more traditional WIMP-based interfaces.

multiplierz v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data.

PubMed

Alexander, William M; Ficarro, Scott B; Adelmant, Guillaume; Marto, Jarrod A

2017-08-01

The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data. New features include support for a wider range of native mass spectrometry file types, interfaces to additional database search engines, compatibility with new reporting formats, and high-level tools to perform post-search proteomic analyses. A GUI desktop environment, mzDesktop, provides access to multiplierz functionality through a user friendly interface. multiplierz is available for download from: https://github.com/BlaisProteomics/multiplierz; and mzDesktop is available for download from: https://sourceforge.net/projects/multiplierz/. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Information System through ANIS at CeSAM

NASA Astrophysics Data System (ADS)

Moreau, C.; Agneray, F.; Gimenez, S.

2015-09-01

ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

Construction of a Simple Low-Cost Teslameter and Its Use with Arduino and MakerPlot Software

ERIC Educational Resources Information Center

Atkin, Keith

2016-01-01

This paper shows how it is possible to construct a very simple device for the measurement of magnetic flux densities in an educational context. It is also shown how such a device can be interfaced to a microcontroller with plotting-software to facilitate the study of magnetic fields produced by a current-carrying coil.

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data.

PubMed

Abelson, Sagi

2014-02-24

In the past decade, the field of molecular biology has become increasingly quantitative; rapid development of new technologies enables researchers to investigate and address fundamental issues quickly and in an efficient manner which were once impossible. Among these technologies, DNA microarray provides methodology for many applications such as gene discovery, diseases diagnosis, drug development and toxicological research and it has been used increasingly since it first emerged. Multiple tools have been developed to interpret the high-throughput data produced by microarrays. However, many times, less consideration has been given to the fact that an extensive and effective interpretation requires close interplay between the bioinformaticians who analyze the data and the biologists who generate it. To bridge this gap and to simplify the usability of such tools we developed Eureka-DMA - an easy-to-operate graphical user interface that allows bioinformaticians and bench-biologists alike to initiate analyses as well as to investigate the data produced by DNA microarrays. In this paper, we describe Eureka-DMA, a user-friendly software that comprises a set of methods for the interpretation of gene expression arrays. Eureka-DMA includes methods for the identification of genes with differential expression between conditions; it searches for enriched pathways and gene ontology terms and combines them with other relevant features. It thus enables the full understanding of the data for following testing as well as generating new hypotheses. Here we show two analyses, demonstrating examples of how Eureka-DMA can be used and its capability to produce relevant and reliable results. We have integrated several elementary expression analysis tools to provide a unified interface for their implementation. Eureka-DMA's simple graphical user interface provides effective and efficient framework in which the investigator has the full set of tools for the visualization and interpretation of the data with the option of exporting the analysis results for later use in other platforms. Eureka-DMA is freely available for academic users and can be downloaded at http://blue-meduza.org/Eureka-DMA.

Finding collaborators: toward interactive discovery tools for research network systems.

PubMed

Borromeo, Charles D; Schleyer, Titus K; Becich, Michael J; Hochheiser, Harry

2014-11-04

Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs. The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype. Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS). Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified. Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows.

Finding Collaborators: Toward Interactive Discovery Tools for Research Network Systems

PubMed Central

Schleyer, Titus K; Becich, Michael J; Hochheiser, Harry

2014-01-01

Background Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs. Objective The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype. Methods Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS). Results Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified. Conclusions Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows. PMID:25370463