Tapir: A web interface for transit/eclipse observability

NASA Astrophysics Data System (ADS)

Jensen, Eric

2013-06-01

Tapir is a set of tools, written in Perl, that provides a web interface for showing the observability of periodic astronomical events, such as exoplanet transits or eclipsing binaries. The package provides tools for creating finding charts for each target and airmass plots for each event. The code can access target lists that are stored on-line in a Google spreadsheet or in a local text file.

A web based Radiation Oncology Dose Manager with a rich User Interface developed using AJAX, ruby, dynamic XHTML and the new Yahoo/EXT User Interface Library.

PubMed

Vali, Faisal; Hong, Robert

2007-10-11

With the evolution of AJAX, ruby on rails, advanced dynamic XHTML technologies and the advent of powerful user interface libraries for javascript (EXT, Yahoo User Interface Library), developers now have the ability to provide truly rich interfaces within web browsers, with reasonable effort and without third-party plugins. We designed and developed an example of such a solution. The User Interface allows radiation oncology practices to intuitively manage different dose fractionation schemes by helping estimate total dose to irradiated organs.

Web service activities at the IRIS DMC to support federated and multidisciplinary access

NASA Astrophysics Data System (ADS)

Trabant, Chad; Ahern, Timothy K.

2013-04-01

At the IRIS Data Management Center (DMC) we have developed a suite of web service interfaces to access our large archive of, primarily seismological, time series data and related metadata. The goals of these web services include providing: a) next-generation and easily used access interfaces for our current users, b) access to data holdings in a form usable for non-seismologists, c) programmatic access to facilitate integration into data processing workflows and d) a foundation for participation in federated data discovery and access systems. To support our current users, our services provide access to the raw time series data and metadata or conversions of the raw data to commonly used formats. Our services also support simple, on-the-fly signal processing options that are common first steps in many workflows. Additionally, high-level data products derived from raw data are available via service interfaces. To support data access by researchers unfamiliar with seismic data we offer conversion of the data to broadly usable formats (e.g. ASCII text) and data processing to convert the data to Earth units. By their very nature, web services are programmatic interfaces. Combined with ubiquitous support for web technologies in programming & scripting languages and support in many computing environments, web services are very well suited for integrating data access into data processing workflows. As programmatic interfaces that can return data in both discipline-specific and broadly usable formats, our services are also well suited for participation in federated and brokered systems either specific to seismology or multidisciplinary. Working within the International Federation of Digital Seismograph Networks, the DMC collaborated on the specification of standardized web service interfaces for use at any seismological data center. These data access interfaces, when supported by multiple data centers, will form a foundation on which to build discovery and access mechanisms for data sets spanning multiple centers. To promote the adoption of these standardized services the DMC has developed portable implementations of the software needed to host these interfaces, minimizing the work required at each data center. Within the COOPEUS project framework, the DMC is working with EU partners to install web services implementations at multiple data centers in Europe.

Customizable scientific web-portal for DIII-D nuclear fusion experiment

NASA Astrophysics Data System (ADS)

Abla, G.; Kim, E. N.; Schissel, D. P.

2010-04-01

Increasing utilization of the Internet and convenient web technologies has made the web-portal a major application interface for remote participation and control of scientific instruments. While web-portals have provided a centralized gateway for multiple computational services, the amount of visual output often is overwhelming due to the high volume of data generated by complex scientific instruments and experiments. Since each scientist may have different priorities and areas of interest in the experiment, filtering and organizing information based on the individual user's need can increase the usability and efficiency of a web-portal. DIII-D is the largest magnetic nuclear fusion device in the US. A web-portal has been designed to support the experimental activities of DIII-D researchers worldwide. It offers a customizable interface with personalized page layouts and list of services for users to select. Each individual user can create a unique working environment to fit his own needs and interests. Customizable services are: real-time experiment status monitoring, diagnostic data access, interactive data analysis and visualization. The web-portal also supports interactive collaborations by providing collaborative logbook, and online instant announcement services. The DIII-D web-portal development utilizes multi-tier software architecture, and Web 2.0 technologies and tools, such as AJAX and Django, to develop a highly-interactive and customizable user interface.

Web-based Hyper Suprime-Cam Data Providing System

NASA Astrophysics Data System (ADS)

Koike, M.; Furusawa, H.; Takata, T.; Price, P.; Okura, Y.; Yamada, Y.; Yamanoi, H.; Yasuda, N.; Bickerton, S.; Katayama, N.; Mineo, S.; Lupton, R.; Bosch, J.; Loomis, C.

2014-05-01

We describe a web-based user interface to retrieve Hyper Suprime-Cam data products, including images and. Users can access data directly from a graphical user interface or by writing a database SQL query. The system provides raw images, reduced images and stacked images (from multiple individual exposures), with previews available. Catalog queries can be executed in preview or queue mode, allowing for both exploratory and comprehensive investigations.

Adding a Visualization Feature to Web Search Engines: It’s Time

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

Wong, Pak C.

Since the first world wide web (WWW) search engine quietly entered our lives in 1994, the “information need” behind web searching has rapidly grown into a multi-billion dollar business that dominates the internet landscape, drives e-commerce traffic, propels global economy, and affects the lives of the whole human race. Today’s search engines are faster, smarter, and more powerful than those released just a few years ago. With the vast investment pouring into research and development by leading web technology providers and the intense emotion behind corporate slogans such as “win the web” or “take back the web,” I can’t helpmore » but ask why are we still using the very same “text-only” interface that was used 13 years ago to browse our search engine results pages (SERPs)? Why has the SERP interface technology lagged so far behind in the web evolution when the corresponding search technology has advanced so rapidly? In this article I explore some current SERP interface issues, suggest a simple but practical visual-based interface design approach, and argue why a visual approach can be a strong candidate for tomorrow’s SERP interface.« less

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.

The World-Wide Web and Mosaic: An Overview for Librarians.

ERIC Educational Resources Information Center

Morgan, Eric Lease

1994-01-01

Provides an overview of the Internet's World-Wide Web (Web), a hypertext system. Highlights include the client/server model; Uniform Resource Locator; examples of software; Web servers versus Gopher servers; HyperText Markup Language (HTML); converting files; Common Gateway Interface; organizing Web information; and the role of librarians in…

Availability of the OGC geoprocessing standard: March 2011 reality check

NASA Astrophysics Data System (ADS)

Lopez-Pellicer, Francisco J.; Rentería-Agualimpia, Walter; Béjar, Rubén; Muro-Medrano, Pedro R.; Zarazaga-Soria, F. Javier

2012-10-01

This paper presents an investigation about the servers available in March 2011 conforming to the Web Processing Service interface specification published by the geospatial standards organization Open Geospatial Consortium (OGC) in 2007. This interface specification gives support to standard Web-based geoprocessing. The data used in this research were collected using a focused crawler configured for finding OGC Web services. The research goals are (i) to provide a reality check of the availability of Web Processing Service servers, (ii) to provide quantitative data about the use of different features defined in the standard that are relevant for a scalable Geoprocessing Web (e.g. long-running processes, Web-accessible data outputs), and (iii) to test if the advances in the use of search engines and focused crawlers for finding Web services can be applied for finding geoscience processing systems. Research results show the feasibility of the discovery approach and provide data about the implementation of the Web Processing Service specification. These results also show extensive use of features related to scalability, except for those related to technical and semantic interoperability.

76 FR 10628 - Self-Regulatory Organizations; the Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Change Regarding Providing Participants With a New Optional Settlement Web Interface February 22, 2011... Rule Change The proposed rule change will establish a new browser-based interface, the ``Settlement Web... Browser System (``PBS'').\\4\\ Based on request from its Participants, DTC has created a more user-friendly...

Using a web-based application to define the accuracy of diagnostic tests when the gold standard is imperfect.

PubMed

Lim, Cherry; Wannapinij, Prapass; White, Lisa; Day, Nicholas P J; Cooper, Ben S; Peacock, Sharon J; Limmathurotsakul, Direk

2013-01-01

Estimates of the sensitivity and specificity for new diagnostic tests based on evaluation against a known gold standard are imprecise when the accuracy of the gold standard is imperfect. Bayesian latent class models (LCMs) can be helpful under these circumstances, but the necessary analysis requires expertise in computational programming. Here, we describe open-access web-based applications that allow non-experts to apply Bayesian LCMs to their own data sets via a user-friendly interface. Applications for Bayesian LCMs were constructed on a web server using R and WinBUGS programs. The models provided (http://mice.tropmedres.ac) include two Bayesian LCMs: the two-tests in two-population model (Hui and Walter model) and the three-tests in one-population model (Walter and Irwig model). Both models are available with simplified and advanced interfaces. In the former, all settings for Bayesian statistics are fixed as defaults. Users input their data set into a table provided on the webpage. Disease prevalence and accuracy of diagnostic tests are then estimated using the Bayesian LCM, and provided on the web page within a few minutes. With the advanced interfaces, experienced researchers can modify all settings in the models as needed. These settings include correlation among diagnostic test results and prior distributions for all unknown parameters. The web pages provide worked examples with both models using the original data sets presented by Hui and Walter in 1980, and by Walter and Irwig in 1988. We also illustrate the utility of the advanced interface using the Walter and Irwig model on a data set from a recent melioidosis study. The results obtained from the web-based applications were comparable to those published previously. The newly developed web-based applications are open-access and provide an important new resource for researchers worldwide to evaluate new diagnostic tests.

WebMeV | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Web MeV (Multiple-experiment Viewer) is a web/cloud-based tool for genomic data analysis. Web MeV is being built to meet the challenge of exploring large public genomic data set with intuitive graphical interface providing access to state-of-the-art analytical tools.

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

PubMed

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

2000-01-01

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

Implementation of an Embedded Web Server Application for Wireless Control of Brain Computer Interface Based Home Environments.

PubMed

Aydın, Eda Akman; Bay, Ömer Faruk; Güler, İnan

2016-01-01

Brain Computer Interface (BCI) based environment control systems could facilitate life of people with neuromuscular diseases, reduces dependence on their caregivers, and improves their quality of life. As well as easy usage, low-cost, and robust system performance, mobility is an important functionality expected from a practical BCI system in real life. In this study, in order to enhance users' mobility, we propose internet based wireless communication between BCI system and home environment. We designed and implemented a prototype of an embedded low-cost, low power, easy to use web server which is employed in internet based wireless control of a BCI based home environment. The embedded web server provides remote access to the environmental control module through BCI and web interfaces. While the proposed system offers to BCI users enhanced mobility, it also provides remote control of the home environment by caregivers as well as the individuals in initial stages of neuromuscular disease. The input of BCI system is P300 potentials. We used Region Based Paradigm (RBP) as stimulus interface. Performance of the BCI system is evaluated on data recorded from 8 non-disabled subjects. The experimental results indicate that the proposed web server enables internet based wireless control of electrical home appliances successfully through BCIs.

Developer Network

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

2012-08-21

NREL's Developer Network, developer.nrel.gov, provides data that users can access to provide data to their own analyses, mobile and web applications. Developers can retrieve the data through a Web services API (application programming interface). The Developer Network handles overhead of serving up web services such as key management, authentication, analytics, reporting, documentation standards, and throttling in a common architecture, while allowing web services and APIs to be maintained and managed independently.

A New User Interface for On-Demand Customizable Data Products for Sensors in a SensorWeb

NASA Technical Reports Server (NTRS)

Mandl, Daniel; Cappelaere, Pat; Frye, Stuart; Sohlberg, Rob; Ly, Vuong; Chien, Steve; Sullivan, Don

2011-01-01

A SensorWeb is a set of sensors, which can consist of ground, airborne and space-based sensors interoperating in an automated or autonomous collaborative manner. The NASA SensorWeb toolbox, developed at NASA/GSFC in collaboration with NASA/JPL, NASA/Ames and other partners, is a set of software and standards that (1) enables users to create virtual private networks of sensors over open networks; (2) provides the capability to orchestrate their actions; (3) provides the capability to customize the output data products and (4) enables automated delivery of the data products to the users desktop. A recent addition to the SensorWeb Toolbox is a new user interface, together with web services co-resident with the sensors, to enable rapid creation, loading and execution of new algorithms for processing sensor data. The web service along with the user interface follows the Open Geospatial Consortium (OGC) standard called Web Coverage Processing Service (WCPS). This presentation will detail the prototype that was built and how the WCPS was tested against a HyspIRI flight testbed and an elastic computation cloud on the ground with EO-1 data. HyspIRI is a future NASA decadal mission. The elastic computation cloud stores EO-1 data and runs software similar to Amazon online shopping.

A GIS-Interface Web Site: Exploratory Learning for Geography Curriculum

ERIC Educational Resources Information Center

Huang, Kuo Hung

2011-01-01

Although Web-based instruction provides learners with sufficient resources for self-paced learning, previous studies have confirmed that browsing navigation-oriented Web sites possibly hampers users' comprehension of information. Web sites designed as "categories of materials" for navigation demand more cognitive effort from users to orient their…

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

NASA Astrophysics Data System (ADS)

Buszko, Marian L.; Buszko, Dominik; Wang, Daniel C.

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance.

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

Since April 2004 the EarthScope USArray seismic network has grown to over 850 broadband stations that stream multi-channel data in near real-time to the Array Network Facility in San Diego. Providing secure, yet open, access to real-time and archived data for a broad range of audiences is best served by a series of platform agnostic low-latency web-based applications. We present a framework of tools that mediate between the world wide web and Boulder Real Time Technologies Antelope Environmental Monitoring System data acquisition and archival software. These tools provide comprehensive information to audiences ranging from network operators and geoscience researchers, to funding agencies and the general public. This ranges from network-wide to station-specific metadata, state-of-health metrics, event detection rates, archival data and dynamic report generation over a station's two year life span. Leveraging open source web-site development frameworks for both the server side (Perl, Python and PHP) and client-side (Flickr, Google Maps/Earth and jQuery) facilitates the development of a robust extensible architecture that can be tailored on a per-user basis, with rapid prototyping and development that adheres to web-standards. Typical seismic data warehouses allow online users to query and download data collected from regional networks, without the scientist directly visually assessing data coverage and/or quality. Using a suite of web-based protocols, we have recently developed an online seismic waveform interface that directly queries and displays data from a relational database through a web-browser. Using the Python interface to Datascope and the Python-based Twisted network package on the server side, and the jQuery Javascript framework on the client side to send and receive asynchronous waveform queries, we display broadband seismic data using the HTML Canvas element that is globally accessible by anyone using a modern web-browser. We are currently creating additional interface tools to create a rich-client interface for accessing and displaying seismic data that can be deployed to any system running the Antelope Real Time System. The software is freely available from the Antelope contributed code Git repository (http://www.antelopeusersgroup.org).

Component, Context, and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2012-11-01

123 5.1 MML Population and Web Service Interface...104 Table 41. Relevant Questions with Associated Web Services...the models, and implementing web services that provide semantically aware programmatic access to the models, including implementing the MS&T

[A web-based biomedical image mosaicing system].

PubMed

Zhang, Meng; Yan, Zhuang-zhi; Pan, Zhi-jun; Shao, Shi-jie

2006-11-01

This paper describes a web service for biomedical image mosaicing. A web site based on CGI (Common Gateway Interface) is implemented. The system is based on Browser/Server model and is tested in www. Finally implementation examples and experiment results are provided.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

PubMed Central

2011-01-01

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

Caching strategies for improving performance of web-based Geographic applications

NASA Astrophysics Data System (ADS)

Liu, M.; Brodzik, M.; Collins, J. A.; Lewis, S.; Oldenburg, J.

2012-12-01

The NASA Operation IceBridge mission collects airborne remote sensing measurements to bridge the gap between NASA's Ice, Cloud and Land Elevation Satellite (ICESat) mission and the upcoming ICESat-2 mission. The IceBridge Data Portal from the National Snow and Ice Data Center provides an intuitive web interface for accessing IceBridge mission observations and measurements. Scientists and users usually do not have knowledge about the individual campaigns but are interested in data collected in a specific place. We have developed a high-performance map interface to allow users to quickly zoom to an area of interest and see any Operation IceBridge overflights. The map interface consists of two layers: the user can pan and zoom on the base map layer; the flight line layer that overlays the base layer provides all the campaign missions that intersect with the current map view. The user can click on the flight campaigns and download the data as needed. The OpenGIS® Web Map Service Interface Standard (WMS) provides a simple HTTP interface for requesting geo-registered map images from one or more distributed geospatial databases. Web Feature Service (WFS) provides an interface allowing requests for geographical features across the web using platform-independent calls. OpenLayers provides vector support (points, polylines and polygons) to build a WMS/WFS client for displaying both layers on the screen. Map Server, an open source development environment for building spatially enabled internet applications, is serving the WMS and WFS spatial data to OpenLayers. Early releases of the portal displayed unacceptably poor load time performance for flight lines and the base map tiles. This issue was caused by long response times from the map server in generating all map tiles and flight line vectors. We resolved the issue by implementing various caching strategies on top of the WMS and WFS services, including the use of Squid (www.squid-cache.org) to cache frequently-used content. Our presentation includes the architectural design of the application, and how we use OpenLayers, WMS and WFS with Squid to build a responsive web application capable of efficiently displaying geospatial data to allow the user to quickly interact with the displayed information. We describe the design, implementation and performance improvement of our caching strategies, and the tools and techniques developed to assist our data caching strategies.

Focused sunlight factor of forest fire danger assessment using Web-GIS and RS technologies

NASA Astrophysics Data System (ADS)

Baranovskiy, Nikolay V.; Sherstnyov, Vladislav S.; Yankovich, Elena P.; Engel, Marina V.; Belov, Vladimir V.

2016-08-01

Timiryazevskiy forestry of Tomsk region (Siberia, Russia) is a study area elaborated in current research. Forest fire danger assessment is based on unique technology using probabilistic criterion, statistical data on forest fires, meteorological conditions, forest sites classification and remote sensing data. MODIS products are used for estimating some meteorological conditions and current forest fire situation. Geonformation technologies are used for geospatial analysis of forest fire danger situation on controlled forested territories. GIS-engine provides opportunities to construct electronic maps with different levels of forest fire probability and support raster layer for satellite remote sensing data on current forest fires. Web-interface is used for data loading on specific web-site and for forest fire danger data representation via World Wide Web. Special web-forms provide interface for choosing of relevant input data in order to process the forest fire danger data and assess the forest fire probability.

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.

A Prototype Visualization of Real-time River Drainage Network Response to Rainfall

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2011-12-01

The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to and visualization of flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, and other flood-related data for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS streams rainfall data from NEXRAD radar, and provides three interfaces including animation for rainfall intensity, daily rainfall totals and rainfall accumulations for past 14 days for Iowa. A real-time interactive visualization interface is developed using past rainfall intensity data. The interface creates community-based rainfall products on-demand using watershed boundaries of each community as a mask. Each individual rainfall pixel is tracked in the interface along the drainage network, and the ones drains to same pixel location are accumulated. The interface loads recent rainfall data in five minute intervals that are combined with current values. Latest web technologies are utilized for the development of the interface including HTML 5 Canvas, and JavaScript. The performance of the interface is optimized to run smoothly on modern web browsers. The interface controls allow users to change internal parameters of the system, and operation conditions of the animation. The interface will help communities understand the effects of rainfall on water transport in stream and river networks and make better-informed decisions regarding the threat of floods. This presentation provides an overview of a unique visualization interface and discusses future plans for real-time dynamic presentations of streamflow forecasting.

Virtual Observatory Interfaces to the Chandra Data Archive

NASA Astrophysics Data System (ADS)

Tibbetts, M.; Harbo, P.; Van Stone, D.; Zografou, P.

2014-05-01

The Chandra Data Archive (CDA) plays a central role in the operation of the Chandra X-ray Center (CXC) by providing access to Chandra data. Proprietary interfaces have been the backbone of the CDA throughout the Chandra mission. While these interfaces continue to provide the depth and breadth of mission specific access Chandra users expect, the CXC has been adding Virtual Observatory (VO) interfaces to the Chandra proposal catalog and observation catalog. VO interfaces provide standards-based access to Chandra data through simple positional queries or more complex queries using the Astronomical Data Query Language. Recent development at the CDA has generalized our existing VO services to create a suite of services that can be configured to provide VO interfaces to any dataset. This approach uses a thin web service layer for the individual VO interfaces, a middle-tier query component which is shared among the VO interfaces for parsing, scheduling, and executing queries, and existing web services for file and data access. The CXC VO services provide Simple Cone Search (SCS), Simple Image Access (SIA), and Table Access Protocol (TAP) implementations for both the Chandra proposal and observation catalogs within the existing archive architecture. Our work with the Chandra proposal and observation catalogs, as well as additional datasets beyond the CDA, illustrates how we can provide configurable VO services to extend core archive functionality.

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

PubMed

Buszko; Buszko; Wang

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance. Copyright 1998 Academic Press.

The APA Style Converter: a Web-based interface for converting articles to APA style for publication.

PubMed

Li, Ping; Cunningham, Krystal

2005-05-01

The APA Style Converter is a Web-based tool with which authors may prepare their articles in APA style according to the APA Publication Manual (5th ed.). The Converter provides a user-friendly interface that allows authors to copy and paste text and upload figures through the Web, and it automatically converts all texts, references, and figures to a structured article in APA style. The output is saved in PDF or RTF format, ready for either electronic submission or hardcopy printing.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

A demanding web-based PACS supported by web services technology

NASA Astrophysics Data System (ADS)

Costa, Carlos M. A.; Silva, Augusto; Oliveira, José L.; Ribeiro, Vasco G.; Ribeiro, José

2006-03-01

During the last years, the ubiquity of web interfaces have pushed practically all PACS suppliers to develop client applications in which clinical practitioners can receive and analyze medical images, using conventional personal computers and Web browsers. However, due to security and performance issues, the utilization of these software packages has been restricted to Intranets. Paradigmatically, one of the most important advantages of digital image systems is to simplify the widespread sharing and remote access of medical data between healthcare institutions. This paper analyses the traditional PACS drawbacks that contribute to their reduced usage in the Internet and describes a PACS based on Web Services technology that supports a customized DICOM encoding syntax and a specific compression scheme providing all historical patient data in a unique Web interface.

Making Your Tools Useful to a Broader Audience

NASA Astrophysics Data System (ADS)

Lyness, M. D.; Broten, M. J.

2006-12-01

With the increasing growth of Web Services and SOAP the ability to connect and reuse computational and also visualization tools from all over the world via Web Interfaces that can be easily displayed in any current browser has provided the means to construct an ideal online research environment. The age-old question of usability is a major determining factor whether a particular tool would find great success in its community. An interface that can be understood purely by a user's intuition is desirable and more closely obtainable than ever before. Through the use of increasingly sophisticated web-oriented technologies including JavaScript, AJAX, and the DOM, web interfaces are able to harness the advantages of the Internet along with the functional capabilities of native applications such as menus, partial page changes, background processing, and visual effects to name a few. Also, with computers becoming a normal part of the educational process companies, such as Google and Microsoft, give us a synthetic intuition as a foundation for new designs. Understanding the way earth science researchers know how to use computers will allow the VLab portal (http://vlab.msi.umn.edu) and other projects to create interfaces that will get used. To provide detailed communication with the users of VLab's computational tools, projects like the Porky Portlet (http://www.gorerle.com/vlab-wiki/index.php?title=Porky_Portlet) spawned to empower users with a fully- detailed, interactive visual representation of progressing workflows. With the well-thought design of such tools and interfaces, researchers around the world will become accustomed to new highly engaging, visual web- based research environments.

User Interface Design in Medical Distributed Web Applications.

PubMed

Serban, Alexandru; Crisan-Vida, Mihaela; Mada, Leonard; Stoicu-Tivadar, Lacramioara

2016-01-01

User interfaces are important to facilitate easy learning and operating with an IT application especially in the medical world. An easy to use interface has to be simple and to customize the user needs and mode of operation. The technology in the background is an important tool to accomplish this. The present work aims to creating a web interface using specific technology (HTML table design combined with CSS3) to provide an optimized responsive interface for a complex web application. In the first phase, the current icMED web medical application layout is analyzed, and its structure is designed using specific tools, on source files. In the second phase, a new graphic adaptable interface to different mobile terminals is proposed, (using HTML table design (TD) and CSS3 method) that uses no source files, just lines of code for layout design, improving the interaction in terms of speed and simplicity. For a complex medical software application a new prototype layout was designed and developed using HTML tables. The method uses a CSS code with only CSS classes applied to one or multiple HTML table elements, instead of CSS styles that can be applied to just one DIV tag at once. The technique has the advantage of a simplified CSS code, and a better adaptability to different media resolutions compared to DIV-CSS style method. The presented work is a proof that adaptive web interfaces can be developed just using and combining different types of design methods and technologies, using HTML table design, resulting in a simpler to learn and use interface, suitable for healthcare services.

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

DOE PAGES

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; ...

2016-08-31

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2, a web toolmore » that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.« less

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

PubMed

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; Juan, Liran; Jiang, Qinghua; Wang, Yadong; Chen, Jin

2016-08-31

The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. We present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/ .

Solar Irradiance Data Products at the LASP Interactive Solar IRradiance Datacenter (LISIRD)

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Ware DeWolfe, A.; Wilson, A.; Pankratz, C. K.; Snow, M. A.; Woods, T. N.

2011-12-01

The Laboratory for Atmospheric and Space Physics (LASP) has developed the LASP Interactive Solar IRradiance Datacenter (LISIRD, http://lasp.colorado.edu/lisird/) web site to provide access to a comprehensive set of solar irradiance measurements and related datasets. Current data holdings include products from NASA missions SORCE, UARS, SME, and TIMED-SEE. The data provided covers a wavelength range from soft X-ray (XUV) at 0.1 nm up to the near infrared (NIR) at 2400 nm, as well as Total Solar Irradiance (TSI). Other datasets include solar indices, spectral and flare models, solar images, and more. The LISIRD web site features updated plotting, browsing, and download capabilities enabled by dygraphs, JavaScript, and Ajax calls to the LASP Time Series Server (LaTiS). In addition to the web browser interface, most of the LISIRD datasets can be accessed via the LaTiS web service interface that supports the OPeNDAP standard. OPeNDAP clients and other programming APIs are available for making requests that subset, aggregate, or filter data on the server before it is transported to the user. This poster provides an overview of the LISIRD system, summarizes the datasets currently available, and provides details on how to access solar irradiance data products through LISIRD's interfaces.

InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang

Here, the Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation. As a result, we present InteGO2, a web toolmore » that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks. In conclusion, InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface.« less

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

PubMed

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

PubMed Central

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

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.

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

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.

Job submission and management through web services: the experience with the CREAM service

NASA Astrophysics Data System (ADS)

Aiftimiei, C.; Andreetto, P.; Bertocco, S.; Fina, S. D.; Ronco, S. D.; Dorigo, A.; Gianelle, A.; Marzolla, M.; Mazzucato, M.; Sgaravatto, M.; Verlato, M.; Zangrando, L.; Corvo, M.; Miccio, V.; Sciaba, A.; Cesini, D.; Dongiovanni, D.; Grandi, C.

2008-07-01

Modern Grid middleware is built around components providing basic functionality, such as data storage, authentication, security, job management, resource monitoring and reservation. In this paper we describe the Computing Resource Execution and Management (CREAM) service. CREAM provides a Web service-based job execution and management capability for Grid systems; in particular, it is being used within the gLite middleware. CREAM exposes a Web service interface allowing conforming clients to submit and manage computational jobs to a Local Resource Management System. We developed a special component, called ICE (Interface to CREAM Environment) to integrate CREAM in gLite. ICE transfers job submissions and cancellations from the Workload Management System, allowing users to manage CREAM jobs from the gLite User Interface. This paper describes some recent studies aimed at assessing the performance and reliability of CREAM and ICE; those tests have been performed as part of the acceptance tests for integration of CREAM and ICE in gLite. We also discuss recent work towards enhancing CREAM with a BES and JSDL compliant interface.

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

PubMed Central

Miller, Benjamin T.; Singh, Rishi P.; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S.; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R.; Woodcock, H. Lee

2014-01-01

This article describes the development, implementation, and use of web-based “lessons” to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that “point and click” simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance. PMID:25057988

Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

PubMed

Miller, Benjamin T; Singh, Rishi P; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R; Woodcock, H Lee

2014-07-01

This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

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,...).

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.

HAWQS Beta Flyer

EPA Pesticide Factsheets

HAWQS is a web-based interactive water quantity and quality modeling system that provides users with interactive web interfaces and maps; pre-loaded input data; outputs that include tables, charts, graphs and raw output data; and a user guide.

HAWQS beta flyer

EPA Pesticide Factsheets

HAWQS is a web-based interactive water quantity and quality modeling system that provides users with interactive web interfaces and maps; pre-loaded input data; outputs that include tables, charts, graphs and raw output data; and a user guide.

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

Candey, R.; Chimiak, R.; Harris, B.; Johnson, R.; Kovalick, T.; Lal, N.; Leckner, H.; Liu, M.; McGuire, R.; Papitashvili, N.;

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

Novel Web-based Education Platforms for Information Communication utilizing Gamification, Virtual and Immersive Reality

NASA Astrophysics Data System (ADS)

Demir, I.

2015-12-01

Recent developments in internet technologies make it possible to manage and visualize large data on the web. Novel visualization techniques and interactive user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. This presentation showcase information communication interfaces, games, and virtual and immersive reality applications for supporting teaching and learning of concepts in atmospheric and hydrological sciences. The information communication platforms utilizes latest web technologies and allow accessing and visualizing large scale data on the web. The simulation system is a web-based 3D interactive learning environment for teaching hydrological and atmospheric processes and concepts. The simulation systems provides a visually striking platform with realistic terrain and weather information, and water simulation. The web-based simulation system provides an environment for students to learn about the earth science processes, and effects of development and human activity on the terrain. Users can access the system in three visualization modes including virtual reality, augmented reality, and immersive reality using heads-up display. The system provides various scenarios customized to fit the age and education level of various users.

Students Using a Novel Web-Based Laboratory Class Support System: A Case Study in Food Chemistry Education

ERIC Educational Resources Information Center

van der Kolk, Koos; Beldman, Gerrit; Hartog, Rob; Gruppen, Harry

2012-01-01

The design, usage, and evaluation of a Web-based laboratory manual (WebLM) are described. The main aim of the WebLM is to support students while working in the laboratory by providing them with just-in-time information. Design guidelines for this electronic manual were derived from literature on cognitive load and user interface design. The WebLM…

Ensemble: a web-based system for psychology survey and experiment management.

PubMed

Tomic, Stefan T; Janata, Petr

2007-08-01

We provide a description of Ensemble, a suite of Web-integrated modules for managing and analyzing data associated with psychology experiments in a small research lab. The system delivers interfaces via a Web browser for creating and presenting simple surveys without the need to author Web pages and with little or no programming effort. The surveys may be extended by selecting and presenting auditory and/or visual stimuli with MATLAB and Flash to enable a wide range of psychophysical and cognitive experiments which do not require the recording of precise reaction times. Additionally, one is provided with the ability to administer and present experiments remotely. The software technologies employed by the various modules of Ensemble are MySQL, PHP, MATLAB, and Flash. The code for Ensemble is open source and available to the public, so that its functions can be readily extended by users. We describe the architecture of the system, the functionality of each module, and provide basic examples of the interfaces.

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

Chemozart: a web-based 3D molecular structure editor and visualizer platform.

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user-friendly interface is composed. More than 30 packages are used to compose this application which adds enough flexibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (application programming interface). JavaScript libraries which allow creation of web pages containing interactive three-dimensional molecular structures has also been made available. The application has been released under Apache 2 License and is available from the project website https://chemozart.com.

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

Information Architecture for the Web: The IA Matrix Approach to Designing Children's Portals.

ERIC Educational Resources Information Center

Large, Andrew; Beheshti, Jamshid; Cole, Charles

2002-01-01

Presents a matrix that can serve as a tool for designing the information architecture of a Web portal in a logical and systematic manner. Highlights include interfaces; metaphors; navigation; interaction; information retrieval; and an example of a children's Web portal to provide access to museum information. (Author/LRW)

Advanced Query and Data Mining Capabilities for MaROS

NASA Technical Reports Server (NTRS)

Wang, Paul; Wallick, Michael N.; Allard, Daniel A.; Gladden, Roy E.; Hy, Franklin H.

2013-01-01

The Mars Relay Operational Service (MaROS) comprises a number of tools to coordinate, plan, and visualize various aspects of the Mars Relay network. These levels include a Web-based user interface, a back-end "ReSTlet" built in Java, and databases that store the data as it is received from the network. As part of MaROS, the innovators have developed and implemented a feature set that operates on several levels of the software architecture. This new feature is an advanced querying capability through either the Web-based user interface, or through a back-end REST interface to access all of the data gathered from the network. This software is not meant to replace the REST interface, but to augment and expand the range of available data. The current REST interface provides specific data that is used by the MaROS Web application to display and visualize the information; however, the returned information from the REST interface has typically been pre-processed to return only a subset of the entire information within the repository, particularly only the information that is of interest to the GUI (graphical user interface). The new, advanced query and data mining capabilities allow users to retrieve the raw data and/or to perform their own data processing. The query language used to access the repository is a restricted subset of the structured query language (SQL) that can be built safely from the Web user interface, or entered as freeform SQL by a user. The results are returned in a CSV (Comma Separated Values) format for easy exporting to third party tools and applications that can be used for data mining or user-defined visualization and interpretation. This is the first time that a service is capable of providing access to all cross-project relay data from a single Web resource. Because MaROS contains the data for a variety of missions from the Mars network, which span both NASA and ESA, the software also establishes an access control list (ACL) on each data record in the database repository to enforce user access permissions through a multilayered approach.

Embedded Web Technology: Applying World Wide Web Standards to Embedded Systems

NASA Technical Reports Server (NTRS)

Ponyik, Joseph G.; York, David W.

2002-01-01

Embedded Systems have traditionally been developed in a highly customized manner. The user interface hardware and software along with the interface to the embedded system are typically unique to the system for which they are built, resulting in extra cost to the system in terms of development time and maintenance effort. World Wide Web standards have been developed in the passed ten years with the goal of allowing servers and clients to intemperate seamlessly. The client and server systems can consist of differing hardware and software platforms but the World Wide Web standards allow them to interface without knowing about the details of system at the other end of the interface. Embedded Web Technology is the merging of Embedded Systems with the World Wide Web. Embedded Web Technology decreases the cost of developing and maintaining the user interface by allowing the user to interface to the embedded system through a web browser running on a standard personal computer. Embedded Web Technology can also be used to simplify an Embedded System's internal network.

High school students as a seismic network analysts

NASA Astrophysics Data System (ADS)

Filatov, P.; Fedorenko, Yu.; Beketova, E.; Husebye, E.

2003-04-01

Many research organizations have a large amount of collected seismological data. Some data centers keep data closed from scientists, others have a specific interfaces for access, what is not acceptable for education. For SeisSchool Network in Norway we have developed an universal interface for research and study. The main principles of our interface are: bullet Accessibility - it should provides data access for everybody any where via Internet without restrictions of hardware platform, operational system, Internet browser or bandwidth of connection. bullet Informativity - it should visualize data, have examples of processing routines (filters, envelopes) including phase picking and event location. Also it provides access to various seismology information. bullet Scalability - provide storage for various types of seismic data and a multitude of services for many user levels. This interface (http://pcg1.ifjf.uib.no) helps analysts in basic research and together with information of our Web site we introduces students to theory and practice of seismology. Based on our Web interface group of students won a Norwegian Young Scientists award. In this presentation we demonstrate advantages of our interface, on-line data processing and how to monitoring our network in near real time.

EPA MED-DULUTH'S ECOTOX AND ECO-SSL WEB APPLICATIONS

EPA Science Inventory

The ECOTOX (ECOTOXicology Database) system developed by the USEPA, National Health and Environmental Effects Research Laboratory (NHEERL), Mid-Continent Ecology Division in Duluth, MN (MED-Duluth), provides a web browser search interface for locating aquatic and terrestrial toxic...

Automating testbed documentation and database access using World Wide Web (WWW) tools

NASA Technical Reports Server (NTRS)

Ames, Charles; Auernheimer, Brent; Lee, Young H.

1994-01-01

A method for providing uniform transparent access to disparate distributed information systems was demonstrated. A prototype testing interface was developed to access documentation and information using publicly available hypermedia tools. The prototype gives testers a uniform, platform-independent user interface to on-line documentation, user manuals, and mission-specific test and operations data. Mosaic was the common user interface, and HTML (Hypertext Markup Language) provided hypertext capability.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.

PubMed

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-08-25

Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

PubMed Central

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

Satisfiers and Dissatisfiers: A Two-Factor Model for Website Design and Evaluation.

ERIC Educational Resources Information Center

Zhang, Ping; von Dran, Gisela M.

2000-01-01

Investigates Web site design factors and their impact from a theoretical perspective. Presents a two-factor model that can guide Web site design and evaluation. According to the model, there are two types of design factors: hygiene and motivator. Results showed that the two-factor model provides a means for Web-user interface studies. Provides…

3DNOW: Image-Based 3d Reconstruction and Modeling via Web

NASA Astrophysics Data System (ADS)

Tefera, Y.; Poiesi, F.; Morabito, D.; Remondino, F.; Nocerino, E.; Chippendale, P.

2018-05-01

This paper presents a web-based 3D imaging pipeline, namely 3Dnow, that can be used by anyone without the need of installing additional software other than a browser. By uploading a set of images through the web interface, 3Dnow can generate sparse and dense point clouds as well as mesh models. 3D reconstructed models can be downloaded with standard formats or previewed directly on the web browser through an embedded visualisation interface. In addition to reconstructing objects, 3Dnow offers the possibility to evaluate and georeference point clouds. Reconstruction statistics, such as minimum, maximum and average intersection angles, point redundancy and density can also be accessed. The paper describes all features available in the web service and provides an analysis of the computational performance using servers with different GPU configurations.

Integrated web-based viewing and secure remote access to a clinical data repository and diverse clinical systems.

PubMed

Duncan, R G; Saperia, D; Dulbandzhyan, R; Shabot, M M; Polaschek, J X; Jones, D T

2001-01-01

The advent of the World-Wide-Web protocols and client-server technology has made it easy to build low-cost, user-friendly, platform-independent graphical user interfaces to health information systems and to integrate the presentation of data from multiple systems. The authors describe a Web interface for a clinical data repository (CDR) that was moved from concept to production status in less than six months using a rapid prototyping approach, multi-disciplinary development team, and off-the-shelf hardware and software. The system has since been expanded to provide an integrated display of clinical data from nearly 20 disparate information systems.

A Pilot Study of the Interface Design of Cross-Cultural Web Sites through Usability Testing of Multilanguage Web Sites and Determining the Preferences of Taiwanese and American Users

ERIC Educational Resources Information Center

Ku, David Tawei; Chang, Chia-Chi

2014-01-01

By conducting usability testing on a multilanguage Web site, this study analyzed the cultural differences between Taiwanese and American users in the performance of assigned tasks. To provide feasible insight into cross-cultural Web site design, Microsoft Office Online (MOO) that supports both traditional Chinese and English and contains an almost…

Analysis Tool Web Services from the EMBL-EBI.

PubMed

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

2013-07-01

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

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

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

2013-01-01

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

[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.

The New Web-Based Hera Data Processing System at the HEASARC

NASA Technical Reports Server (NTRS)

Pence, W.

2011-01-01

The HEASARC at NASA/GSFC has provide an on-line astronomical data processing system called Hera for several years. Hera provides a complete data processing environment, including installed software packages, local data storage, and the CPU resources needed to process the user's data. The original design of Hera, however, has 2 requirements that has limited it's usefulness for some users, namely, that 1) the user must download and install a small helper program on their own computer before using Hera, and 2) Hera requires that several computer ports/sockets be allowed to communicate through any local firewalls on the users machine. Both of these restrictions can be problematic for some users, therefore we are now migrating Hera into a purely Web based environment which only requires a standard Web browser. The first release of Web Hera is now publicly available at http://heasarc.gsfc.nasa.gov/webheara/. It currently provides a standard graphical interface for running hundreds of different data processing programs that are available in the HEASARC's ftools software package. Over the next year we to add more features to Web Hera, including an interactive command line interface, and more display and line capabilities.

77 FR 61039 - Self-Regulatory Organizations; NASDAQ OMX PHLX LLC; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-05

... adopt the new QView service. QView is a web-based, front-end application, which provides a subscribing... orders and executions provided in the QView dashboard interface. The dashboard also allows a QView... trading activity.\\5\\ \\4\\ TradeInfo PSX is a web-based tool that, among other things, allows users access...

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

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

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

User interface and patient involvement.

PubMed

Andreassen, Hege Kristin; Lundvoll Nilsen, Line

2013-01-01

Increased patient involvement is a goal in contemporary health care, and of importance to the development of patient oriented ICT. In this paper we discuss how the design of patient-user interfaces can affect patient involvement. Our discussion is based on 12 semi-structured interviews with patient users of a web-based solution for patient--doctor communication piloted in Norway. We argue ICT solutions offering a choice of user interfaces on the patient side are preferable to ensure individual accommodation and a high degree of patient involvement. When introducing web-based tools for patient--health professional communication a free-text option should be provided to the patient users.

A Web-based interface to calculate phonotactic probability for words and nonwords in English

PubMed Central

VITEVITCH, MICHAEL S.; LUCE, PAUL A.

2008-01-01

Phonotactic probability refers to the frequency with which phonological segments and sequences of phonological segments occur in words in a given language. We describe one method of estimating phonotactic probabilities based on words in American English. These estimates of phonotactic probability have been used in a number of previous studies and are now being made available to other researchers via a Web-based interface. Instructions for using the interface, as well as details regarding how the measures were derived, are provided in the present article. The Phonotactic Probability Calculator can be accessed at http://www.people.ku.edu/~mvitevit/PhonoProbHome.html. PMID:15641436

BioServices: a common Python package to access biological Web Services programmatically.

PubMed

Cokelaer, Thomas; Pultz, Dennis; Harder, Lea M; Serra-Musach, Jordi; Saez-Rodriguez, Julio

2013-12-15

Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework. BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming. BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Web servers and services for electrostatics calculations with APBS and PDB2PQR

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

Unni, Samir; Huang, Yong; Hanson, Robert M.

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in currentmore » distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.« less

Web servers and services for electrostatics calculations with APBS and PDB2PQR

PubMed Central

Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

2011-01-01

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

The Design and Application of a Web-Based Self- And Peer-Assessment System

ERIC Educational Resources Information Center

Sung, Yao-Ting; Chang, Kuo-En; Chiou, Shen-Kuan; Hou, Huei-Tse

2005-01-01

This study describes the web-based self- and peer-assessments system, or the Web-SPA, which has been shown to provide teachers with a flexible interface with which to arrange various self- and peer-assessment procedures. Secondly, this study examines the effects of the application of the progressively focused self- and peer-assessment (PFSPA)…

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

PubMed Central

Jiao, Xiaoli; Sherman, Brad T.; Huang, Da Wei; Stephens, Robert; Baseler, Michael W.; Lane, H. Clifford; Lempicki, Richard A.

2012-01-01

Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. Availability: The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html. Contact: xiaoli.jiao@nih.gov; rlempicki@nih.gov PMID:22543366

DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

PubMed

Jiao, Xiaoli; Sherman, Brad T; Huang, Da Wei; Stephens, Robert; Baseler, Michael W; Lane, H Clifford; Lempicki, Richard A

2012-07-01

The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html.

Development of Web GIS for complex processing and visualization of climate geospatial datasets as an integral part of dedicated Virtual Research Environment

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Okladnikov, Igor; Titov, Alexander

2017-04-01

For comprehensive usage of large geospatial meteorological and climate datasets it is necessary to create a distributed software infrastructure based on the spatial data infrastructure (SDI) approach. Currently, it is generally accepted that the development of client applications as integrated elements of such infrastructure should be based on the usage of modern web and GIS technologies. The paper describes the Web GIS for complex processing and visualization of geospatial (mainly in NetCDF and PostGIS formats) datasets as an integral part of the dedicated Virtual Research Environment for comprehensive study of ongoing and possible future climate change, and analysis of their implications, providing full information and computing support for the study of economic, political and social consequences of global climate change at the global and regional levels. The Web GIS consists of two basic software parts: 1. Server-side part representing PHP applications of the SDI geoportal and realizing the functionality of interaction with computational core backend, WMS/WFS/WPS cartographical services, as well as implementing an open API for browser-based client software. Being the secondary one, this part provides a limited set of procedures accessible via standard HTTP interface. 2. Front-end part representing Web GIS client developed according to a "single page application" technology based on JavaScript libraries OpenLayers (http://openlayers.org/), ExtJS (https://www.sencha.com/products/extjs), GeoExt (http://geoext.org/). It implements application business logic and provides intuitive user interface similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Boundless/OpenGeo architecture was used as a basis for Web-GIS client development. According to general INSPIRE requirements to data visualization Web GIS provides such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. The specialized Web GIS client contains three basic tires: • Tier of NetCDF metadata in JSON format • Middleware tier of JavaScript objects implementing methods to work with: o NetCDF metadata o XML file of selected calculations configuration (XML task) o WMS/WFS/WPS cartographical services • Graphical user interface tier representing JavaScript objects realizing general application business logic Web-GIS developed provides computational processing services launching to support solving tasks in the area of environmental monitoring, as well as presenting calculation results in the form of WMS/WFS cartographical layers in raster (PNG, JPG, GeoTIFF), vector (KML, GML, Shape), and binary (NetCDF) formats. It has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical formats. The work is supported by the Russian Science Foundation grant No 16-19-10257.

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

PubMed Central

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

2012-01-01

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

New web technologies for astronomy

NASA Astrophysics Data System (ADS)

Sprimont, P.-G.; Ricci, D.; Nicastro, L.

2014-12-01

Thanks to the new HTML5 capabilities and the huge improvements of the JavaScript language, it is now possible to design very complex and interactive web user interfaces. On top of that, the once monolithic and file-server oriented web servers are evolving into easily programmable server applications capable to cope with the complex interactions made possible by the new generation of browsers. We believe that the whole community of amateur and professionals astronomers can benefit from the potential of these new technologies. New web interfaces can be designed to provide the user with a large deal of much more intuitive and interactive tools. Accessing astronomical data archives, schedule, control and monitor observatories, and in particular robotic telescopes, supervising data reduction pipelines, all are capabilities that can now be implemented in a JavaScript web application. In this paper we describe the Sadira package we are implementing exactly to this aim.

IMAGESEER - IMAGEs for Education and Research

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

AstrodyToolsWeb an e-Science project in Astrodynamics and Celestial Mechanics fields

NASA Astrophysics Data System (ADS)

López, R.; San-Juan, J. F.

2013-05-01

Astrodynamics Web Tools, AstrodyToolsWeb (http://tastrody.unirioja.es), is an ongoing collaborative Web Tools computing infrastructure project which has been specially designed to support scientific computation. AstrodyToolsWeb provides project collaborators with all the technical and human facilities in order to wrap, manage, and use specialized noncommercial software tools in Astrodynamics and Celestial Mechanics fields, with the aim of optimizing the use of resources, both human and material. However, this project is open to collaboration from the whole scientific community in order to create a library of useful tools and their corresponding theoretical backgrounds. AstrodyToolsWeb offers a user-friendly web interface in order to choose applications, introduce data, and select appropriate constraints in an intuitive and easy way for the user. After that, the application is executed in real time, whenever possible; then the critical information about program behavior (errors and logs) and output, including the postprocessing and interpretation of its results (graphical representation of data, statistical analysis or whatever manipulation therein), are shown via the same web interface or can be downloaded to the user's computer.

Semantically-enabled sensor plug & play for the sensor web.

PubMed

Bröring, Arne; Maúe, Patrick; Janowicz, Krzysztof; Nüst, Daniel; Malewski, Christian

2011-01-01

Environmental sensors have continuously improved by becoming smaller, cheaper, and more intelligent over the past years. As consequence of these technological advancements, sensors are increasingly deployed to monitor our environment. The large variety of available sensor types with often incompatible protocols complicates the integration of sensors into observing systems. The standardized Web service interfaces and data encodings defined within OGC's Sensor Web Enablement (SWE) framework make sensors available over the Web and hide the heterogeneous sensor protocols from applications. So far, the SWE framework does not describe how to integrate sensors on-the-fly with minimal human intervention. The driver software which enables access to sensors has to be implemented and the measured sensor data has to be manually mapped to the SWE models. In this article we introduce a Sensor Plug & Play infrastructure for the Sensor Web by combining (1) semantic matchmaking functionality, (2) a publish/subscribe mechanism underlying the SensorWeb, as well as (3) a model for the declarative description of sensor interfaces which serves as a generic driver mechanism. We implement and evaluate our approach by applying it to an oil spill scenario. The matchmaking is realized using existing ontologies and reasoning engines and provides a strong case for the semantic integration capabilities provided by Semantic Web research.

Semantically-Enabled Sensor Plug & Play for the Sensor Web

PubMed Central

Bröring, Arne; Maúe, Patrick; Janowicz, Krzysztof; Nüst, Daniel; Malewski, Christian

2011-01-01

Environmental sensors have continuously improved by becoming smaller, cheaper, and more intelligent over the past years. As consequence of these technological advancements, sensors are increasingly deployed to monitor our environment. The large variety of available sensor types with often incompatible protocols complicates the integration of sensors into observing systems. The standardized Web service interfaces and data encodings defined within OGC’s Sensor Web Enablement (SWE) framework make sensors available over the Web and hide the heterogeneous sensor protocols from applications. So far, the SWE framework does not describe how to integrate sensors on-the-fly with minimal human intervention. The driver software which enables access to sensors has to be implemented and the measured sensor data has to be manually mapped to the SWE models. In this article we introduce a Sensor Plug & Play infrastructure for the Sensor Web by combining (1) semantic matchmaking functionality, (2) a publish/subscribe mechanism underlying the SensorWeb, as well as (3) a model for the declarative description of sensor interfaces which serves as a generic driver mechanism. We implement and evaluate our approach by applying it to an oil spill scenario. The matchmaking is realized using existing ontologies and reasoning engines and provides a strong case for the semantic integration capabilities provided by Semantic Web research. PMID:22164033

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

PubMed

Simovski, Boris; Kanduri, Chakravarthi; Gundersen, Sveinung; Titov, Dmytro; Domanska, Diana; Bock, Christoph; Bossini-Castillo, Lara; Chikina, Maria; Favorov, Alexander; Layer, Ryan M; Mironov, Andrey A; Quinlan, Aaron R; Sheffield, Nathan C; Trynka, Gosia; Sandve, Geir K

2018-06-05

Functional genomics assays produce sets of genomic regions as one of their main outputs. To biologically interpret such region-sets, researchers often use colocalization analysis, where the statistical significance of colocalization (overlap, spatial proximity) between two or more region-sets is tested. Existing colocalization analysis tools vary in the statistical methodology and analysis approaches, thus potentially providing different conclusions for the same research question. As the findings of colocalization analysis are often the basis for follow-up experiments, it is helpful to use several tools in parallel and to compare the results. We developed the Coloc-stats web service to facilitate such analyses. Coloc-stats provides a unified interface to perform colocalization analysis across various analytical methods and method-specific options (e.g. colocalization measures, resolution, null models). Coloc-stats helps the user to find a method that supports their experimental requirements and allows for a straightforward comparison across methods. Coloc-stats is implemented as a web server with a graphical user interface that assists users with configuring their colocalization analyses. Coloc-stats is freely available at https://hyperbrowser.uio.no/coloc-stats/.

Wilber 3: A Python-Django Web Application For Acquiring Large-scale Event-oriented Seismic Data

NASA Astrophysics Data System (ADS)

Newman, R. L.; Clark, A.; Trabant, C. M.; Karstens, R.; Hutko, A. R.; Casey, R. E.; Ahern, T. K.

2013-12-01

Since 2001, the IRIS Data Management Center (DMC) WILBER II system has provided a convenient web-based interface for locating seismic data related to a particular event, and requesting a subset of that data for download. Since its launch, both the scale of available data and the technology of web-based applications have developed significantly. Wilber 3 is a ground-up redesign that leverages a number of public and open-source projects to provide an event-oriented data request interface with a high level of interactivity and scalability for multiple data types. Wilber 3 uses the IRIS/Federation of Digital Seismic Networks (FDSN) web services for event data, metadata, and time-series data. Combining a carefully optimized Google Map with the highly scalable SlickGrid data API, the Wilber 3 client-side interface can load tens of thousands of events or networks/stations in a single request, and provide instantly responsive browsing, sorting, and filtering of event and meta data in the web browser, without further reliance on the data service. The server-side of Wilber 3 is a Python-Django application, one of over a dozen developed in the last year at IRIS, whose common framework, components, and administrative overhead represent a massive savings in developer resources. Requests for assembled datasets, which may include thousands of data channels and gigabytes of data, are queued and executed using the Celery distributed Python task scheduler, giving Wilber 3 the ability to operate in parallel across a large number of nodes.

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.

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

Chao, Tian-Jy; Kim, Younghun

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented thatmore » communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.« less

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).

Semantic Annotations and Querying of Web Data Sources

NASA Astrophysics Data System (ADS)

Hornung, Thomas; May, Wolfgang

A large part of the Web, actually holding a significant portion of the useful information throughout the Web, consists of views on hidden databases, provided by numerous heterogeneous interfaces that are partly human-oriented via Web forms ("Deep Web"), and partly based on Web Services (only machine accessible). In this paper we present an approach for annotating these sources in a way that makes them citizens of the Semantic Web. We illustrate how queries can be stated in terms of the ontology, and how the annotations are used to selected and access appropriate sources and to answer the queries.

Development of Virtual Resource Based IoT Proxy for Bridging Heterogeneous Web Services in IoT Networks.

PubMed

Jin, Wenquan; Kim, DoHyeun

2018-05-26

The Internet of Things is comprised of heterogeneous devices, applications, and platforms using multiple communication technologies to connect the Internet for providing seamless services ubiquitously. With the requirement of developing Internet of Things products, many protocols, program libraries, frameworks, and standard specifications have been proposed. Therefore, providing a consistent interface to access services from those environments is difficult. Moreover, bridging the existing web services to sensor and actuator networks is also important for providing Internet of Things services in various industry domains. In this paper, an Internet of Things proxy is proposed that is based on virtual resources to bridge heterogeneous web services from the Internet to the Internet of Things network. The proxy enables clients to have transparent access to Internet of Things devices and web services in the network. The proxy is comprised of server and client to forward messages for different communication environments using the virtual resources which include the server for the message sender and the client for the message receiver. We design the proxy for the Open Connectivity Foundation network where the virtual resources are discovered by the clients as Open Connectivity Foundation resources. The virtual resources represent the resources which expose services in the Internet by web service providers. Although the services are provided by web service providers from the Internet, the client can access services using the consistent communication protocol in the Open Connectivity Foundation network. For discovering the resources to access services, the client also uses the consistent discovery interface to discover the Open Connectivity Foundation devices and virtual resources.

Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

ERIC Educational Resources Information Center

Perri, M. J.; Weber, S. H.

2014-01-01

A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

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

EPA Science Inventory

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

Open Science Grid (OSG) Ticket Synchronization: Keeping Your Home Field Advantage In A Distributed Environment

NASA Astrophysics Data System (ADS)

Gross, Kyle; Hayashi, Soichi; Teige, Scott; Quick, Robert

2012-12-01

Large distributed computing collaborations, such as the Worldwide LHC Computing Grid (WLCG), face many issues when it comes to providing a working grid environment for their users. One of these is exchanging tickets between various ticketing systems in use by grid collaborations. Ticket systems such as Footprints, RT, Remedy, and ServiceNow all have different schema that must be addressed in order to provide a reliable exchange of information between support entities and users in different grid environments. To combat this problem, OSG Operations has created a ticket synchronization interface called GOC-TX that relies on web services instead of error-prone email parsing methods of the past. Synchronizing tickets between different ticketing systems allows any user or support entity to work on a ticket in their home environment, thus providing a familiar and comfortable place to provide updates without having to learn another ticketing system. The interface is built in a way that it is generic enough that it can be customized for nearly any ticketing system with a web-service interface with only minor changes. This allows us to be flexible and rapidly bring new ticket synchronization online. Synchronization can be triggered by different methods including mail, web services interface, and active messaging. GOC-TX currently interfaces with Global Grid User Support (GGUS) for WLCG, Remedy at Brookhaven National Lab (BNL), and Request Tracker (RT) at the Virtual Data Toolkit (VDT). Work is progressing on the Fermi National Accelerator Laboratory (FNAL) ServiceNow synchronization. This paper will explain the problems faced by OSG and how they led OSG to create and implement this ticket synchronization system along with the technical details that allow synchronization to be preformed at a production level.

Characteristics of experiential education web sites of US colleges and schools of pharmacy.

PubMed

Rodgers, Philip T; Leadon, Kim

2013-06-12

To evaluate the characteristics of experiential education Web sites of colleges and schools of pharmacy in the United States. The experiential education Web pages of 124 US colleges and schools of pharmacy were reviewed for office or program name, practice experience management software, experiential education newsletter, practice experience manual, preceptor development programs, new preceptor application processes, and interactive Web site interfaces. The term "office of experiential education" was used by 27.4% of colleges and schools. Fifty percent of the colleges and schools used E-value as their practice experience management software. Only a minority of colleges and schools made experiential manual(s) available online, offered newsletters targeted to preceptors, and/or provided Web site interactive interfaces for preceptor communication. The Preceptors Training and Resource Network was the preceptor development program most frequently promoted. The majority of US colleges and schools of pharmacy have official Web sites for their experiential education program; however, few offer resources online or use interactive or social media to their advantage.

Web-based interactive 2D/3D medical image processing and visualization software.

PubMed

Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

2010-05-01

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

MAGMA: analysis of two-channel microarrays made easy.

PubMed

Rehrauer, Hubert; Zoller, Stefan; Schlapbach, Ralph

2007-07-01

The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch.

A Mediator-Based Approach to Resolving Interface Heterogeneity of Web Services

NASA Astrophysics Data System (ADS)

Leitner, Philipp; Rosenberg, Florian; Michlmayr, Anton; Huber, Andreas; Dustdar, Schahram

In theory, service-oriented architectures are based on the idea of increasing flexibility in the selection of internal and external business partners using loosely-coupled services. However, in practice this flexibility is limited by the fact that partners need not only to provide the same service, but to do so via virtually the same interface in order to actually be interchangeable easily. Invocation-level mediation may be used to overcome this issue — by using mediation interface differences can be resolved transparently at runtime. In this chapter we discuss the basic ideas of mediation, with a focus on interface-level mediation. We show how interface mediation is integrated into our dynamic Web service invocation framework DAIOS, and present three different mediation strategies, one based on structural message similarity, one based on semantically annotated WSDL, and one which is embedded into the VRESCo SOA runtime, a larger research project with explicit support for service mediation.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

Web Based Rapid Mapping of Disaster Areas using Satellite Images, Web Processing Service, Web Mapping Service, Frequency Based Change Detection Algorithm and J-iView

NASA Astrophysics Data System (ADS)

Bandibas, J. C.; Takarada, S.

2013-12-01

Timely identification of areas affected by natural disasters is very important for a successful rescue and effective emergency relief efforts. This research focuses on the development of a cost effective and efficient system of identifying areas affected by natural disasters, and the efficient distribution of the information. The developed system is composed of 3 modules which are the Web Processing Service (WPS), Web Map Service (WMS) and the user interface provided by J-iView (fig. 1). WPS is an online system that provides computation, storage and data access services. In this study, the WPS module provides online access of the software implementing the developed frequency based change detection algorithm for the identification of areas affected by natural disasters. It also sends requests to WMS servers to get the remotely sensed data to be used in the computation. WMS is a standard protocol that provides a simple HTTP interface for requesting geo-registered map images from one or more geospatial databases. In this research, the WMS component provides remote access of the satellite images which are used as inputs for land cover change detection. The user interface in this system is provided by J-iView, which is an online mapping system developed at the Geological Survey of Japan (GSJ). The 3 modules are seamlessly integrated into a single package using J-iView, which could rapidly generate a map of disaster areas that is instantaneously viewable online. The developed system was tested using ASTER images covering the areas damaged by the March 11, 2011 tsunami in northeastern Japan. The developed system efficiently generated a map showing areas devastated by the tsunami. Based on the initial results of the study, the developed system proved to be a useful tool for emergency workers to quickly identify areas affected by natural disasters.

A resource-oriented architecture for a Geospatial Web

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; Nativi, Stefano

2010-05-01

In this presentation we discuss some architectural issues on the design of an architecture for a Geospatial Web, that is an information system for sharing geospatial resources according to the Web paradigm. The success of the Web in building a multi-purpose information space, has raised questions about the possibility of adopting the same approach for systems dedicated to the sharing of more specific resources, such as the geospatial information, that is information characterized by spatial/temporal reference. To this aim an investigation on the nature of the Web and on the validity of its paradigm for geospatial resources is required. The Web was born in the early 90's to provide "a shared information space through which people and machines could communicate" [Berners-Lee 1996]. It was originally built around a small set of specifications (e.g. URI, HTTP, HTML, etc.); however, in the last two decades several other technologies and specifications have been introduced in order to extend its capabilities. Most of them (e.g. the SOAP family) actually aimed to transform the Web in a generic Distributed Computing Infrastructure. While these efforts were definitely successful enabling the adoption of service-oriented approaches for machine-to-machine interactions supporting complex business processes (e.g. for e-Government and e-Business applications), they do not fit in the original concept of the Web. In the year 2000, R. T. Fielding, one of the designers of the original Web specifications, proposes a new architectural style for distributed systems, called REST (Representational State Transfer), aiming to capture the fundamental characteristics of the Web as it was originally conceived [Fielding 2000]. In this view, the nature of the Web lies not so much in the technologies, as in the way they are used. Maintaining the Web architecture conform to the REST style would then assure the scalability, extensibility and low entry barrier of the original Web. On the contrary, systems using the same Web technologies and specifications but according to a different architectural style, despite their usefulness, should not be considered part of the Web. If the REST style captures the significant Web characteristics, then, in order to build a Geospatial Web it is necessary that its architecture satisfies all the REST constraints. One of them is of particular importance: the adoption of a Uniform Interface. It prescribes that all the geospatial resources must be accessed through the same interface; moreover according to the REST style this interface must satisfy four further constraints: a) identification of resources; b) manipulation of resources through representations; c) self-descriptive messages; and, d) hypermedia as the engine of application state. In the Web, the uniform interface provides basic operations which are meaningful for generic resources. They typically implement the CRUD pattern (Create-Retrieve-Update-Delete) which demonstrated to be flexible and powerful in several general-purpose contexts (e.g. filesystem management, SQL for database management systems, etc.). Restricting the scope to a subset of resources it would be possible to identify other generic actions which are meaningful for all of them. For example for geospatial resources, subsetting, resampling, interpolation and coordinate reference systems transformations functionalities are candidate functionalities for a uniform interface. However an investigation is needed to clarify the semantics of those actions for different resources, and consequently if they can really ascend the role of generic interface operation. Concerning the point a), (identification of resources), it is required that every resource addressable in the Geospatial Web has its own identifier (e.g. a URI). This allows to implement citation and re-use of resources, simply providing the URI. OPeNDAP and KVP encodings of OGC data access services specifications might provide a basis for it. Concerning point b) (manipulation of resources through representations), the Geospatial Web poses several issues. In fact, while the Web mainly handles semi-structured information, in the Geospatial Web the information is typically structured with several possible data models (e.g. point series, gridded coverages, trajectories, etc.) and encodings. A possibility would be to simplify the interchange formats, choosing to support a subset of data models and format(s). This is what actually the Web designers did choosing to define a common format for hypermedia (HTML), although the underlying protocol would be generic. Concerning point c), self-descriptive messages, the exchanged messages should describe themselves and their content. This would not be actually a major issue considering the effort put in recent years on geospatial metadata models and specifications. The point d), hypermedia as the engine of application state, is actually where the Geospatial Web would mainly differ from existing geospatial information sharing systems. In fact the existing systems typically adopt a service-oriented architecture, where applications are built as a single service or as a workflow of services. On the other hand, in the Geospatial Web, applications should be built following the path between interconnected resources. The link between resources should be made explicit as hyperlinks. The adoption of Semantic Web solutions would allow to define not only the existence of a link between two resources, but also the nature of the link. The implementation of a Geospatial Web would allow to build an information system with the same characteristics of the Web sharing its points-of-strength and weaknesses. The main advantages would be the following: • The user would interact with the Geospatial Web according to the well-known Web navigation paradigm. This would lower the barrier to the access to geospatial applications for non-specialists (e.g. the success of Google Maps and other Web mapping applications); • Successful Web and Web 2.0 applications - search engines, feeds, social network - could be integrated/replicated in the Geospatial Web; The main drawbacks would be the following: • The Uniform Interface simplifies the overall system architecture (e.g. no service registry, and service descriptors required), but moves the complexity to the data representation. Moreover since the interface must stay generic, it results really simple and therefore complex interactions would require several transfers. • In the geospatial domain one of the most valuable resources are processes (e.g. environmental models). How they can be modeled as resources accessed through the common interface is an open issue. Taking into account advantages and drawback it seems that a Geospatial Web would be useful, but its use would be limited to specific use-cases not covering all the possible applications. The Geospatial Web architecture could be partly based on existing specifications, while other aspects need investigation. References [Berners-Lee 1996] T. Berners-Lee, "WWW: Past, present, and future". IEEE Computer, 29(10), Oct. 1996, pp. 69-77. [Fielding 2000] Fielding, R. T. 2000. Architectural styles and the design of network-based software architectures. PhD Dissertation. Dept. of Information and Computer Science, University of California, Irvine

A web interface for easy flexible protein-protein docking with ATTRACT.

PubMed

de Vries, Sjoerd J; Schindler, Christina E M; Chauvot de Beauchêne, Isaure; Zacharias, Martin

2015-02-03

Protein-protein docking programs can give valuable insights into the structure of protein complexes in the absence of an experimental complex structure. Web interfaces can facilitate the use of docking programs by structural biologists. Here, we present an easy web interface for protein-protein docking with the ATTRACT program. While aimed at nonexpert users, the web interface still covers a considerable range of docking applications. The web interface supports systematic rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibility. The execution of a docking protocol takes up to a few hours on a standard desktop computer. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

GeoNetwork powered GI-cat: a geoportal hybrid solution

NASA Astrophysics Data System (ADS)

Baldini, Alessio; Boldrini, Enrico; Santoro, Mattia; Mazzetti, Paolo

2010-05-01

To the aim of setting up a Spatial Data Infrastructures (SDI) the creation of a system for the metadata management and discovery plays a fundamental role. An effective solution is the use of a geoportal (e.g. FAO/ESA geoportal), that has the important benefit of being accessible from a web browser. With this work we present a solution based integrating two of the available frameworks: GeoNetwork and GI-cat. GeoNetwork is an opensource software designed to improve accessibility of a wide variety of data together with the associated ancillary information (metadata), at different scale and from multidisciplinary sources; data are organized and documented in a standard and consistent way. GeoNetwork implements both the Portal and Catalog components of a Spatial Data Infrastructure (SDI) defined in the OGC Reference Architecture. It provides tools for managing and publishing metadata on spatial data and related services. GeoNetwork allows harvesting of various types of web data sources e.g. OGC Web Services (e.g. CSW, WCS, WMS). GI-cat is a distributed catalog based on a service-oriented framework of modular components and can be customized and tailored to support different deployment scenarios. It can federate a multiplicity of catalogs services, as well as inventory and access services in order to discover and access heterogeneous ESS resources. The federated resources are exposed by GI-cat through several standard catalog interfaces (e.g. OGC CSW AP ISO, OpenSearch, etc.) and by the GI-cat extended interface. Specific components implement mediation services for interfacing heterogeneous service providers, each of which exposes a specific standard specification; such components are called Accessors. These mediating components solve providers data modelmultiplicity by mapping them onto the GI-cat internal data model which implements the ISO 19115 Core profile. Accessors also implement the query protocol mapping; first they translate the query requests expressed according to the interface protocols exposed by GI-cat into the multiple query dialects spoken by the resource service providers. Currently, a number of well-accepted catalog and inventory services are supported, including several OGC Web Services, THREDDS Data Server, SeaDataNet Common Data Index, GBIF and OpenSearch engines. A GeoNetwork powered GI-cat has been developed in order to exploit the best of the two frameworks. The new system uses a modified version of GeoNetwork web interface in order to add the capability of querying also the specified GI-cat catalog and not only the GeoNetwork internal database. The resulting system consists in a geoportal in which GI-cat plays the role of the search engine. This new system allows to distribute the query on the different types of data sources linked to a GI-cat. The metadata results of the query are then visualized by the Geonetwork web interface. This configuration was experimented in the framework of GIIDA, a project of the Italian National Research Council (CNR) focused on data accessibility and interoperability. A second advantage of this solution is achieved setting up a GeoNetwork catalog amongst the accessors of the GI-cat instance. Such a configuration will allow in turn GI-cat to run the query against the internal GeoNetwork database. This allows to have both the harvesting and the metadata editor functionalities provided by GeoNetwork and the distributed search functionality of GI-cat available in a consistent way through the same web interface.

Search Interface Design Using Faceted Indexing for Web Resources.

ERIC Educational Resources Information Center

Devadason, Francis; Intaraksa, Neelawat; Patamawongjariya, Pornprapa; Desai, Kavita

2001-01-01

Describes an experimental system designed to organize and provide access to Web documents using a faceted pre-coordinate indexing system based on the Deep Structure Indexing System (DSIS) derived from POPSI (Postulate based Permuted Subject Indexing) of Bhattacharyya, and the facet analysis and chain indexing system of Ranganathan. (AEF)

A new reference implementation of the PSICQUIC web service.

PubMed

del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

2013-07-01

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

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.

Haptic interface of web-based training system for interventional radiology procedures

NASA Astrophysics Data System (ADS)

Ma, Xin; Lu, Yiping; Loe, KiaFock; Nowinski, Wieslaw L.

2004-05-01

The existing web-based medical training systems and surgical simulators can provide affordable and accessible medical training curriculum, but they seldom offer the trainee realistic and affordable haptic feedback. Therefore, they cannot offer the trainee a suitable practicing environment. In this paper, a haptic solution for interventional radiology (IR) procedures is proposed. System architecture of a web-based training system for IR procedures is briefly presented first. Then, the mechanical structure, the working principle and the application of a haptic device are discussed in detail. The haptic device works as an interface between the training environment and the trainees and is placed at the end user side. With the system, the user can be trained on the interventional radiology procedures - navigating catheters, inflating balloons, deploying coils and placing stents on the web and get surgical haptic feedback in real time.

The ATS Web Page Provides "Tool Boxes" for: Access Opportunities, Performance, Interfaces, Volume, Environments, "Wish List" Entry and Educational Outreach

NASA Technical Reports Server (NTRS)

1999-01-01

This viewgraph presentation gives an overview of the Access to Space website, including information on the 'tool boxes' available on the website for access opportunities, performance, interfaces, volume, environments, 'wish list' entry, and educational outreach.

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

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

End-to-end interoperability and workflows from building architecture design to one or more simulations

DOEpatents

Chao, Tian-Jy; Kim, Younghun

2015-02-10

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented that communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.

Guide to the Internet. The world wide web.

PubMed Central

Pallen, M.

1995-01-01

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals. Images p1554-a Fig 5 PMID:8520402

Are Pretty Interfaces Worth the Time? The Effects of User Interface Types on Web-Based Instruction

ERIC Educational Resources Information Center

Cheon, Jongpil; Grant, Michael M.

2009-01-01

The purpose of this study was to examine the effectiveness of three different interface types on Web-based instruction: a text-based interface, a graphical interface and a metaphorical interface. In order to determine differences among three interface groups, we compared learning performance, cognitive load, usability, and appeal with various data…

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Application of Microsoft's ActiveX and DirectX technologies to the visulization of physical system dynamics

NASA Astrophysics Data System (ADS)

Mann, Christopher; Narasimhamurthi, Natarajan

1998-08-01

This paper discusses a specific implementation of a web and complement based simulation systems. The overall simulation container is implemented within a web page viewed with Microsoft's Internet Explorer 4.0 web browser. Microsoft's ActiveX/Distributed Component Object Model object interfaces are used in conjunction with the Microsoft DirectX graphics APIs to provide visualization functionality for the simulation. The MathWorks' Matlab computer aided control system design program is used as an ActiveX automation server to provide the compute engine for the simulations.

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

NWS Hydrologic Information Center: Flood Impact Information

Science.gov Websites

The Hydrologic Information Center Web pages have been modified to provide an interface consistent and navigation modified to make it easier to find information provided by the Hydrologic Information

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance

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

Dong, Han; Sharma, Diksha; Badano, Aldo, E-mail: aldo.badano@fda.hhs.gov

2014-12-15

Purpose: Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridMANTIS, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webMANTIS and visualMANTIS to facilitate the setup of computational experiments via hybridMANTIS. Methods: Themore » visualization tools visualMANTIS and webMANTIS enable the user to control simulation properties through a user interface. In the case of webMANTIS, control via a web browser allows access through mobile devices such as smartphones or tablets. webMANTIS acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. Results: The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridMANTIS. The users can download the output images and statistics through a zip file for future reference. In addition, webMANTIS provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. Conclusions: The visualization tools visualMANTIS and webMANTIS provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.« less

BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

PubMed

Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

2015-06-02

Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

Design Options for Multimodal Web Applications

NASA Astrophysics Data System (ADS)

Stanciulescu, Adrian; Vanderdonckt, Jean

The capabilities of multimodal applications running on the web are well de-lineated since they are mainly constrained by what their underlying standard mark up language offers, as opposed to hand-made multimodal applications. As the experience in developing such multimodal web applications is growing, the need arises to identify and define major design options of such application to pave the way to a structured development life cycle. This paper provides a design space of independent design options for multimodal web applications based on three types of modalities: graphical, vocal, tactile, and combined. On the one hand, these design options may provide designers with some explicit guidance on what to decide or not for their future user interface, while exploring various design alternatives. On the other hand, these design options have been implemented as graph transformations per-formed on a user interface model represented as a graph. Thanks to a transformation engine, it allows designers to play with the different values of each design option, to preview the results of the transformation, and to obtain the corresponding code on-demand

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

PubMed

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

2012-07-01

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

mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

PubMed Central

Lee, Hwan Young; Song, Injee; Ha, Eunho; Cho, Sung-Bae; Yang, Woo Ick; Shin, Kyoung-Jin

2008-01-01

Background For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data. Results We developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode. Conclusion The mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at . PMID:19014619

CliniWeb: managing clinical information on the World Wide Web.

PubMed

Hersh, W R; Brown, K E; Donohoe, L C; Campbell, E M; Horacek, A E

1996-01-01

The World Wide Web is a powerful new way to deliver on-line clinical information, but several problems limit its value to health care professionals: content is highly distributed and difficult to find, clinical information is not separated from non-clinical information, and the current Web technology is unable to support some advanced retrieval capabilities. A system called CliniWeb has been developed to address these problems. CliniWeb is an index to clinical information on the World Wide Web, providing a browsing and searching interface to clinical content at the level of the health care student or provider. Its database contains a list of clinical information resources on the Web that are indexed by terms from the Medical Subject Headings disease tree and retrieved with the assistance of SAPHIRE. Limitations of the processes used to build the database are discussed, together with directions for future research.

IntegratedMap: a Web interface for integrating genetic map data.

PubMed

Yang, Hongyu; Wang, Hongyu; Gingle, Alan R

2005-05-01

IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources. IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp

Optimizing the Information Presentation on Mining Potential by using Web Services Technology with Restful Protocol

NASA Astrophysics Data System (ADS)

Abdillah, T.; Dai, R.; Setiawan, E.

2018-02-01

This study aims to develop the application of Web Services technology with RestFul Protocol to optimize the information presentation on mining potential. This study used User Interface Design approach for the information accuracy and relevance as well as the Web Service for the reliability in presenting the information. The results show that: the information accuracy and relevance regarding mining potential can be seen from the achievement of User Interface implementation in the application that is based on the following rules: The consideration of the appropriate colours and objects, the easiness of using the navigation, and users’ interaction with the applications that employs symbols and languages understood by the users; the information accuracy and relevance related to mining potential can be observed by the information presented by using charts and Tool Tip Text to help the users understand the provided chart/figure; the reliability of the information presentation is evident by the results of Web Services testing in Figure 4.5.6. This study finds out that User Interface Design and Web Services approaches (for the access of different Platform apps) are able to optimize the presentation. The results of this study can be used as a reference for software developers and Provincial Government of Gorontalo.

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").

Web Services and Other Enhancements at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Allen, R. M.

2012-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, or MiniSEED depending on the service, and are compatible with the equivalent IRIS DMC web services. The NCEDC is currently providing the following Web Services: (1) Station inventory and channel response information delivered in StationXML format, (2) Channel response information delivered in RESP format, (3) Time series availability delivered in text and XML formats, (4) Single channel and bulk data request delivered in MiniSEED format. The NCEDC is also developing a rich Earthquake Catalog Web Service to allow users to query earthquake catalogs based on selection parameters such as time, location or geographic region, magnitude, depth, azimuthal gap, and rms. It will return (in QuakeML format) user-specified results that can include simple earthquake parameters, as well as observations such as phase arrivals, codas, amplitudes, and computed parameters such as first motion mechanisms, moment tensors, and rupture length. The NCEDC will work with both IRIS and the International Federation of Digital Seismograph Networks (FDSN) to define a uniform set of web service specifications that can be implemented by multiple data centers to provide users with a common data interface across data centers. The NCEDC now hosts earthquake catalogs and waveforms from the US Department of Energy (DOE) Enhanced Geothermal Systems (EGS) monitoring networks. These data can be accessed through the above web services and through special NCEDC web pages.

Draper Station Analysis Tool

NASA Technical Reports Server (NTRS)

Bedrossian, Nazareth; Jang, Jiann-Woei; McCants, Edward; Omohundro, Zachary; Ring, Tom; Templeton, Jeremy; Zoss, Jeremy; Wallace, Jonathan; Ziegler, Philip

2011-01-01

Draper Station Analysis Tool (DSAT) is a computer program, built on commercially available software, for simulating and analyzing complex dynamic systems. Heretofore used in designing and verifying guidance, navigation, and control systems of the International Space Station, DSAT has a modular architecture that lends itself to modification for application to spacecraft or terrestrial systems. DSAT consists of user-interface, data-structures, simulation-generation, analysis, plotting, documentation, and help components. DSAT automates the construction of simulations and the process of analysis. DSAT provides a graphical user interface (GUI), plus a Web-enabled interface, similar to the GUI, that enables a remotely located user to gain access to the full capabilities of DSAT via the Internet and Webbrowser software. Data structures are used to define the GUI, the Web-enabled interface, simulations, and analyses. Three data structures define the type of analysis to be performed: closed-loop simulation, frequency response, and/or stability margins. DSAT can be executed on almost any workstation, desktop, or laptop computer. DSAT provides better than an order of magnitude improvement in cost, schedule, and risk assessment for simulation based design and verification of complex dynamic systems.

WIFIP: a web-based user interface for automated synchrotron beamlines.

PubMed

Sallaz-Damaz, Yoann; Ferrer, Jean Luc

2017-09-01

The beamline control software, through the associated graphical user interface (GUI), is the user access point to the experiment, interacting with synchrotron beamline components and providing automated routines. FIP, the French beamline for the Investigation of Proteins, is a highly automatized macromolecular crystallography (MX) beamline at the European Synchrotron Radiation Facility. On such a beamline, a significant number of users choose to control their experiment remotely. This is often performed with a limited bandwidth and from a large choice of computers and operating systems. Furthermore, this has to be possible in a rapidly evolving experimental environment, where new developments have to be easily integrated. To face these challenges, a light, platform-independent, control software and associated GUI are required. Here, WIFIP, a web-based user interface developed at FIP, is described. Further than being the present FIP control interface, WIFIP is also a proof of concept for future MX control software.

Introducing the PRIDE Archive RESTful web services.

PubMed

Reisinger, Florian; del-Toro, Noemi; Ternent, Tobias; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-07-01

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

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

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

DOE PAGES

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.; ...

2016-11-11

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

CMR Catalog Service for the Web

NASA Technical Reports Server (NTRS)

Newman, Doug; Mitchell, Andrew

2016-01-01

With the impending retirement of Global Change Master Directory (GCMD) Application Programming Interfaces (APIs) the Common Metadata Repository (CMR) was charged with providing a collection-level Catalog Service for the Web (CSW) that provided the same level of functionality as GCMD. This talk describes the capabilities of the CMR CSW API with particular reference to the support of the Committee on Earth Observation Satellites (CEOS) Working Group on Information Systems and Services (WGISS) Integrated Catalog (CWIC).

A brief introduction to web-based genome browsers.

PubMed

Wang, Jun; Kong, Lei; Gao, Ge; Luo, Jingchu

2013-03-01

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

Learning System of Web Navigation Patterns through Hypertext Probabilistic Grammars

ERIC Educational Resources Information Center

Cortes Vasquez, Augusto

2015-01-01

One issue of real interest in the area of web data mining is to capture users' activities during connection and extract behavior patterns that help define their preferences in order to improve the design of future pages adapting websites interfaces to individual users. This research is intended to provide, first of all, a presentation of the…

XML-Based Visual Specification of Multidisciplinary Applications

NASA Technical Reports Server (NTRS)

Al-Theneyan, Ahmed; Jakatdar, Amol; Mehrotra, Piyush; Zubair, Mohammad

2001-01-01

The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

The Legacy Archive for Microwave Background Data Analysis (LAMBDA)

NASA Astrophysics Data System (ADS)

Miller, Nathan; LAMBDA

2018-01-01

The Legacy Archive for Microwave Background Data Analysis (LAMBDA) provides CMB researchers with archival data for cosmology missions, software tools, and links to other sites of interest. LAMBDA is one-stop shopping for CMB researchers. It hosts data from WMAP along with many suborbital experiments. Over the past year, LAMBDA has acquired new data from SPTpol, SPIDER and ACTPol. In addition to the primary CMB, LAMBDA also provides foreground data.LAMBDA has several ongoing efforts to provide tools for CMB researchers. These tools include a web interface for CAMB and a web interface for a CMB survey footprint database and plotting tool. Additionally, we have recently developed a Docker container with standard CMB analysis tools and demonstrations in the form of Jupyter notebooks. These containers will be publically available through Docker's container repository and the source will be available on github.

Realising the Uncertainty Enabled Model Web

NASA Astrophysics Data System (ADS)

Cornford, D.; Bastin, L.; Pebesma, E. J.; Williams, M.; Stasch, C.; Jones, R.; Gerharz, L.

2012-12-01

The FP7 funded UncertWeb project aims to create the "uncertainty enabled model web". The central concept here is that geospatial models and data resources are exposed via standard web service interfaces, such as the Open Geospatial Consortium (OGC) suite of encodings and interface standards, allowing the creation of complex workflows combining both data and models. The focus of UncertWeb is on the issue of managing uncertainty in such workflows, and providing the standards, architecture, tools and software support necessary to realise the "uncertainty enabled model web". In this paper we summarise the developments in the first two years of UncertWeb, illustrating several key points with examples taken from the use case requirements that motivate the project. Firstly we address the issue of encoding specifications. We explain the usage of UncertML 2.0, a flexible encoding for representing uncertainty based on a probabilistic approach. This is designed to be used within existing standards such as Observations and Measurements (O&M) and data quality elements of ISO19115 / 19139 (geographic information metadata and encoding specifications) as well as more broadly outside the OGC domain. We show profiles of O&M that have been developed within UncertWeb and how UncertML 2.0 is used within these. We also show encodings based on NetCDF and discuss possible future directions for encodings in JSON. We then discuss the issues of workflow construction, considering discovery of resources (both data and models). We discuss why a brokering approach to service composition is necessary in a world where the web service interfaces remain relatively heterogeneous, including many non-OGC approaches, in particular the more mainstream SOAP and WSDL approaches. We discuss the trade-offs between delegating uncertainty management functions to the service interfaces themselves and integrating the functions in the workflow management system. We describe two utility services to address conversion between uncertainty types, and between the spatial / temporal support of service inputs / outputs. Finally we describe the tools being generated within the UncertWeb project, considering three main aspects: i) Elicitation of uncertainties on model inputs. We are developing tools to enable domain experts to provide judgements about input uncertainties from UncertWeb model components (e.g. parameters in meteorological models) which allow panels of experts to engage in the process and reach a consensus view on the current knowledge / beliefs about that parameter or variable. We are developing systems for continuous and categorical variables as well as stationary spatial fields. ii) Visualisation of the resulting uncertain outputs from the end of the workflow, but also at intermediate steps. At this point we have prototype implementations driven by the requirements from the use cases that motivate UncertWeb. iii) Sensitivity and uncertainty analysis on model outputs. Here we show the design of the overall system we are developing, including the deployment of an emulator framework to allow computationally efficient approaches. We conclude with a summary of the open issues and remaining challenges we are facing in UncertWeb, and provide a brief overview of how we plan to tackle these.

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/

WebSat--a web software for microsatellite marker development.

PubMed

Martins, Wellington Santos; Lucas, Divino César Soares; Neves, Kelligton Fabricio de Souza; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. The web tool may be accessed at http://purl.oclc.org/NET/websat/

Unified web-based network management based on distributed object orientated software agents

NASA Astrophysics Data System (ADS)

Djalalian, Amir; Mukhtar, Rami; Zukerman, Moshe

2002-09-01

This paper presents an architecture that provides a unified web interface to managed network devices that support CORBA, OSI or Internet-based network management protocols. A client gains access to managed devices through a web browser, which is used to issue management operations and receive event notifications. The proposed architecture is compatible with both the OSI Management reference Model and CORBA. The steps required for designing the building blocks of such architecture are identified.

Visual Analytics for Law Enforcement: Deploying a Service-Oriented Analytic Framework for Web-based Visualization

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

Dowson, Scott T.; Bruce, Joseph R.; Best, Daniel M.

2009-04-14

This paper presents key components of the Law Enforcement Information Framework (LEIF) that provides communications, situational awareness, and visual analytics tools in a service-oriented architecture supporting web-based desktop and handheld device users. LEIF simplifies interfaces and visualizations of well-established visual analytical techniques to improve usability. Advanced analytics capability is maintained by enhancing the underlying processing to support the new interface. LEIF development is driven by real-world user feedback gathered through deployments at three operational law enforcement organizations in the US. LEIF incorporates a robust information ingest pipeline supporting a wide variety of information formats. LEIF also insulates interface and analyticalmore » components from information sources making it easier to adapt the framework for many different data repositories.« less

WebVR: an interactive web browser for virtual environments

NASA Astrophysics Data System (ADS)

Barsoum, Emad; Kuester, Falko

2005-03-01

The pervasive nature of web-based content has lead to the development of applications and user interfaces that port between a broad range of operating systems and databases, while providing intuitive access to static and time-varying information. However, the integration of this vast resource into virtual environments has remained elusive. In this paper we present an implementation of a 3D Web Browser (WebVR) that enables the user to search the internet for arbitrary information and to seamlessly augment this information into virtual environments. WebVR provides access to the standard data input and query mechanisms offered by conventional web browsers, with the difference that it generates active texture-skins of the web contents that can be mapped onto arbitrary surfaces within the environment. Once mapped, the corresponding texture functions as a fully integrated web-browser that will respond to traditional events such as the selection of links or text input. As a result, any surface within the environment can be turned into a web-enabled resource that provides access to user-definable data. In order to leverage from the continuous advancement of browser technology and to support both static as well as streamed content, WebVR uses ActiveX controls to extract the desired texture skin from industry strength browsers, providing a unique mechanism for data fusion and extensibility.

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.

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

PubMed

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

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

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

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

Role-Based And Adaptive User Interface Designs In A Teledermatology Consult System: A Way To Secure And A Way To Enhance

PubMed Central

Lin, Yi-Jung; Speedie, Stuart

2003-01-01

User interface design is one of the most important parts of developing applications. Nowadays, a quality user interface must not only accommodate interaction between machines and users, but also needs to recognize the differences and provide functionalities for users from role-to-role or even individual-to-individual. With the web-based application of our Teledermatology consult system, the development environment provides us highly useful opportunities to create dynamic user interfaces, which lets us to gain greater access control and has the potential to increase efficiency of the system. We will describe the two models of user interfaces in our system: Role-based and Adaptive. PMID:14728419

A SOAP Web Services Interface to ACE Data

NASA Astrophysics Data System (ADS)

Davis, A. J.; Hamell, G. R.

2005-05-01

Since early in 1998, NASA's Advanced Composition Explorer (ACE) spacecraft has provided continuous measurements of solar wind and energetic particle activity from L1, located approximately 0.01 AU sunward of Earth. ACE data from nine instruments are being used to measure and compare the elemental and isotopic composition of the solar corona, the nearby interstellar medium, and the Galaxy, and to study particle acceleration processes that occur in a wide range of environments. The spacecraft has enough fuel to stay in orbit about L1 until at least 2020. The ACE Science Center (ASC) provides access to ACE data, and performs level 1 and browse data processing for the science instruments. Available on-line are solar wind, solar energetic particle, and galactic cosmic ray intensity and composition data, as well as solar wind and magnetic field parameters on a variety of time scales. We describe our recent efforts to provide enhanced access to ACE data via a SOAP Web Services interface. The interface utilizes the Space Physics Archive Search and Extract (SPASE) dictionary, and will be compatible with emerging virtual observatories.

78 FR 79434 - Notice of Technical Conference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-30

...: one that will allow EQR users to file through a web interface on the Commission's Web site, and a... the conference, staff will demonstrate how to make a filing using both the XML and web interface... Calendar of Events on the Commission's Web site, www.ferc.gov . A free webcast of the conference will be...

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…

Broadband network on-line data acquisition system with web based interface for control and basic analysis

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

Passive seismic experiment "13BB Star" is operated since mid 2013 in northern Poland and consists of 13 broadband seismic stations. One of the elements of this experiment is dedicated on-line data acquisition system comprised of both client (station) side and server side modules with web based interface that allows monitoring of network status and provides tools for preliminary data analysis. Station side is controlled by ARM Linux board that is programmed to maintain 3G/EDGE internet connection, receive data from digitizer, send data do central server among with additional auxiliary parameters like temperatures, voltages and electric current measurements. Station side is controlled by set of easy to install PHP scripts. Data is transmitted securely over SSH protocol to central server. Central server is a dedicated Linux based machine. Its duty is receiving and processing all data from all stations including auxiliary parameters. Server side software is written in PHP and Python. Additionally, it allows remote station configuration and provides web based interface for user friendly interaction. All collected data can be displayed for each day and station. It also allows manual creation of event oriented plots with different filtering abilities and provides numerous status and statistic information. Our solution is very flexible and easy to modify. In this presentation we would like to share our solution and experience. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.

Systemic Vulnerabilities in Customer-Premises Equipment (CPE) Routers

DTIC Science & Technology

2017-07-01

equipment (CPE),1 specifically small office/home office (SOHO) routers, has become ubiquitous. CPE routers are notorious for their web interface...and enabling remote management, although all settings controllable over the web -management interface can be manipulated. • 85% (11 of 13) of...specifically small office/home office (SOHO) routers— has become ubiquitous. CPE routers are notorious for their web interface vulnerabilities, old ver- sions

A Web-based interface to calculate phonotactic probability for words and nonwords in Modern Standard Arabic.

PubMed

Aljasser, Faisal; Vitevitch, Michael S

2018-02-01

A number of databases (Storkel Behavior Research Methods, 45, 1159-1167, 2013) and online calculators (Vitevitch & Luce Behavior Research Methods, Instruments, and Computers, 36, 481-487, 2004) have been developed to provide statistical information about various aspects of language, and these have proven to be invaluable assets to researchers, clinicians, and instructors in the language sciences. The number of such resources for English is quite large and continues to grow, whereas the number of such resources for other languages is much smaller. This article describes the development of a Web-based interface to calculate phonotactic probability in Modern Standard Arabic (MSA). A full description of how the calculator can be used is provided. It can be freely accessed at http://phonotactic.drupal.ku.edu/ .

ICM: a web server for integrated clustering of multi-dimensional biomedical data.

PubMed

He, Song; He, Haochen; Xu, Wenjian; Huang, Xin; Jiang, Shuai; Li, Fei; He, Fuchu; Bo, Xiaochen

2016-07-08

Large-scale efforts for parallel acquisition of multi-omics profiling continue to generate extensive amounts of multi-dimensional biomedical data. Thus, integrated clustering of multiple types of omics data is essential for developing individual-based treatments and precision medicine. However, while rapid progress has been made, methods for integrated clustering are lacking an intuitive web interface that facilitates the biomedical researchers without sufficient programming skills. Here, we present a web tool, named Integrated Clustering of Multi-dimensional biomedical data (ICM), that provides an interface from which to fuse, cluster and visualize multi-dimensional biomedical data and knowledge. With ICM, users can explore the heterogeneity of a disease or a biological process by identifying subgroups of patients. The results obtained can then be interactively modified by using an intuitive user interface. Researchers can also exchange the results from ICM with collaborators via a web link containing a Project ID number that will directly pull up the analysis results being shared. ICM also support incremental clustering that allows users to add new sample data into the data of a previous study to obtain a clustering result. Currently, the ICM web server is available with no login requirement and at no cost at http://biotech.bmi.ac.cn/icm/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

77 FR 18280 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-27

... adopted QView on December 1, 2011 at no cost to subscribers.\\3\\ QView is a Web-based, front-end... executions provided in the QView dashboard interface. The dashboard also allows a QView subscriber to track...\\ \\5\\ TradeInfo is a web-based tool that, among other things, allows users access to all of the NASDAQ...

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

PubMed Central

2014-01-01

Abstract ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data. Reviewers This article was reviewed by Prof. Sandor Pongor, Dr. Yuriy Gusev, and Dr. Shyam Prabhakar (nominated by Prof. Limsoon Wong). PMID:24555784

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

WebEAV

PubMed Central

Nadkarni, Prakash M.; Brandt, Cynthia M.; Marenco, Luis

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples. PMID:10887163

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.

Web-Based Interface for Command and Control of Network Sensors

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Doubleday, Joshua R.; Shams, Khawaja S.

2010-01-01

This software allows for the visualization and control of a network of sensors through a Web browser interface. It is currently being deployed for a network of sensors monitoring Mt. Saint Helen s volcano; however, this innovation is generic enough that it can be deployed for any type of sensor Web. From this interface, the user is able to fully control and monitor the sensor Web. This includes, but is not limited to, sending "test" commands to individual sensors in the network, monitoring for real-world events, and reacting to those events

Using Qualitative Methods to Create a Home Health Web Application User Interface for Patients with Low Computer Proficiency.

PubMed

Baier, Rosa R; Cooper, Emily; Wysocki, Andrea; Gravenstein, Stefan; Clark, Melissa

2015-01-01

Despite the investment in public reporting for a number of healthcare settings, evidence indicates that consumers do not routinely use available data to select providers. This suggests that existing reports do not adequately incorporate recommendations for consumer-facing reports or web applications. Healthcentric Advisors and Brown University undertook a multi-phased approach to create a consumer-facing home health web application in Rhode Island. This included reviewing the evidence base review to identify design recommendations and then creating a paper prototype and wireframe. We performed qualitative research to iteratively test our proposed user interface with two user groups, home health consumers and hospital case managers, refining our design to create the final web application. To test our prototype, we conducted two focus groups, with a total of 13 consumers, and 28 case manager interviews. Both user groups responded favorably to the prototype, with the majority commenting that they felt this type of tool would be useful. Case managers suggested revisions to ensure the application conformed to laws requiring Medicare patients to have the freedom to choose among providers and could be incorporated into hospital workflow. After incorporating changes and creating the wireframe, we conducted usability testing interviews with 14 home health consumers and six hospital case managers. We found that consumers needed prompting to navigate through the wireframe; they demonstrated confusion through both their words and body language. As a result, we modified the web application's sequence, navigation, and function to provide additional instructions and prompts. Although we designed our web application for low literacy and low health literacy, using recommendations from the evidence base, we overestimated the extent to which older adults were familiar with using computers. Some of our key learnings and recommendations run counter to general web design principles, leading us to believe that such guidelines need to be adapted for this user group. As web applications proliferate, it is important to ensure those who are most vulnerable-who have the least knowledge and the lowest literacy, health literacy, and computer proficiency-can access, understand, and use them. In order for the investment in public reporting to produce value, consumer-facing web applications need to be designed to address end users' unique strengths and limitations. Our findings may help others to build consumer-facing tools or technology targeted to a predominantly older population. We encourage others designing consumer-facing web technologies to critically evaluate their assumptions about user interface design, particularly if they are designing tools for older adults, and to test products with their end users.

WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web

PubMed Central

Tudorache, Tania; Nyulas, Csongor; Noy, Natalya F.; Musen, Mark A.

2012-01-01

In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu. PMID:23807872

Ubiquitous remote operation collaborative interface for MRI scanners

NASA Astrophysics Data System (ADS)

Morris, H. Douglas

2001-05-01

We have developed a remote control interface for research class magnetic resonance imaging (MRI) spectrometers. The goal of the interface is to provide a better collaborative environment for geographically dispersed researchers and a tool that can teach students of medical imaging in a network-based laboratory using state-of-the-art MR instrumentation that would not otherwise be available. The interface for the remote operator(s) is now ubiquitous web browser, which was chosen for the ease of controlling the operator interface, the display of both image and text information, and the wide availability on many computer platforms. The remote operator is presented with an active display in which they may select and control most of the parameters in the MRI experiment. The MR parameters are relayed via web browser to a CGI program running in a standard web server, which passes said parameters to the MRI manufacturers control software. The data returned to the operator(s) consists of the parameters used in acquiring that image, a flat 8-bit grayscale GIF representation of the image, and a 16-bit grayscale image that can be viewed by an appropriate application. It is obvious that the utility of this interface would be helpful for researchers of regional and national facilities to more closely collaborate with colleagues across their region, the nation, or the world. And medical imaging students can put much of their classroom discussions into practice on machinery that would not normally be available to them.

Data Access and Web Services at the EarthScope Plate Boundary Observatory

NASA Astrophysics Data System (ADS)

Matykiewicz, J.; Anderson, G.; Henderson, D.; Hodgkinson, K.; Hoyt, B.; Lee, E.; Persson, E.; Torrez, D.; Smith, J.; Wright, J.; Jackson, M.

2007-12-01

The EarthScope Plate Boundary Observatory (PBO) at UNAVCO, Inc., part of the NSF-funded EarthScope project, is designed to study the three-dimensional strain field resulting from deformation across the active boundary zone between the Pacific and North American plates in the western United States. To meet these goals, PBO will install 880 continuous GPS stations, 103 borehole strainmeter stations, and five laser strainmeters, as well as manage data for 209 previously existing continuous GPS stations and one previously existing laser strainmeter. UNAVCO provides access to data products from these stations, as well as general information about the PBO project, via the PBO web site (http://pboweb.unavco.org). GPS and strainmeter data products can be found using a variety of access methods, incuding map searches, text searches, and station specific data retrieval. In addition, the PBO construction status is available via multiple mapping interfaces, including custom web based map widgets and Google Earth. Additional construction details can be accessed from PBO operational pages and station specific home pages. The current state of health for the PBO network is available with the statistical snap-shot, full map interfaces, tabular web based reports, and automatic data mining and alerts. UNAVCO is currently working to enhance the community access to this information by developing a web service framework for the discovery of data products, interfacing with operational engineers, and exposing data services to third party participants. In addition, UNAVCO, through the PBO project, provides advanced data management and monitoring systems for use by the community in operating geodetic networks in the United States and beyond. We will demonstrate these systems during the AGU meeting, and we welcome inquiries from the community at any time.

The Plate Boundary Observatory: Community Focused Web Services

NASA Astrophysics Data System (ADS)

Matykiewicz, J.; Anderson, G.; Lee, E.; Hoyt, B.; Hodgkinson, K.; Persson, E.; Wright, J.; Torrez, D.; Jackson, M.

2006-12-01

The Plate Boundary Observatory (PBO), part of the NSF-funded EarthScope project, is designed to study the three-dimensional strain field resulting from deformation across the active boundary zone between the Pacific and North American plates in the western United States. To meet these goals, PBO will install 852 continuous GPS stations, 103 borehole strainmeter stations, 28 tiltmeters, and five laser strainmeters, as well as manage data for 209 previously existing continuous GPS stations. UNAVCO provides access to data products from these stations, as well as general information about the PBO project, via the PBO web site (http://pboweb.unavco.org). GPS and strainmeter data products can be found using a variety of channels, including map searches, text searches, and station specific data retrieval. In addition, the PBO construction status is available via multiple mapping interfaces, including custom web based map widgets and Google Earth. Additional construction details can be accessed from PBO operational pages and station specific home pages. The current state of health for the PBO network is available with the statistical snap-shot, full map interfaces, tabular web based reports, and automatic data mining and alerts. UNAVCO is currently working to enhance the community access to this information by developing a web service framework for the discovery of data products, interfacing with operational engineers, and exposing data services to third party participants. In addition, UNAVCO, through the PBO project, provides advanced data management and monitoring systems for use by the community in operating geodetic networks in the United States and beyond. We will demonstrate these systems during the AGU meeting, and we welcome inquiries from the community at any time.

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

DTIC Science & Technology

2007-12-01

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

Network Science Research Laboratory (NSRL) Telemetry Warehouse

DTIC Science & Technology

2016-06-01

Functionality and architecture of the NSRL Telemetry Warehouse are also described as well as the web interface, data structure, security aspects, and...Experiment Controller 6 4.5 Telemetry Sensors 7 4.6 Custom Data Processing Nodes 7 5. Web Interface 8 6. Data Structure 8 6.1 Measurements 8...telemetry in comma-separated value (CSV) format from the web interface or via custom applications developed by researchers using the client application

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study

PubMed Central

2018-01-01

Background Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. Objective The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Methods Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. Results All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. Conclusions To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. PMID:29699962

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

PubMed Central

Gao, Jianjiong; Aksoy, Bülent Arman; Dogrusoz, Ugur; Dresdner, Gideon; Gross, Benjamin; Sumer, S. Onur; Sun, Yichao; Jacobsen, Anders; Sinha, Rileen; Larsson, Erik; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2014-01-01

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. PMID:23550210

Brain-controlled applications using dynamic P300 speller matrices.

PubMed

Halder, Sebastian; Pinegger, Andreas; Käthner, Ivo; Wriessnegger, Selina C; Faller, Josef; Pires Antunes, João B; Müller-Putz, Gernot R; Kübler, Andrea

2015-01-01

Access to the world wide web and multimedia content is an important aspect of life. We present a web browser and a multimedia user interface adapted for control with a brain-computer interface (BCI) which can be used by severely motor impaired persons. The web browser dynamically determines the most efficient P300 BCI matrix size to select the links on the current website. This enables control of the web browser with fewer commands and smaller matrices. The multimedia player was based on an existing software. Both applications were evaluated with a sample of ten healthy participants and three end-users. All participants used a visual P300 BCI with face-stimuli for control. The healthy participants completed the multimedia player task with 90% accuracy and the web browsing task with 85% accuracy. The end-users completed the tasks with 62% and 58% accuracy. All healthy participants and two out of three end-users reported that they felt to be in control of the system. In this study we presented a multimedia application and an efficient web browser implemented for control with a BCI. Both applications provide access to important areas of modern information retrieval and entertainment. Copyright © 2014 Elsevier B.V. All rights reserved.

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interactive Web-based Floodplain Simulation System for Realistic Experiments of Flooding and Flood Damage

NASA Astrophysics Data System (ADS)

Demir, I.

2013-12-01

Recent developments in web technologies make it easy to manage and visualize large data sets with general public. Novel visualization techniques and dynamic user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The floodplain simulation system is a web-based 3D interactive flood simulation environment to create real world flooding scenarios. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create and modify predefined scenarios, control environmental parameters, and evaluate flood mitigation techniques. The web-based simulation system provides an environment to children and adults learn about the flooding, flood damage, and effects of development and human activity in the floodplain. The system provides various scenarios customized to fit the age and education level of the users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various flooding and land use scenarios.

Earthdata User Interface Patterns: Building Usable Web Interfaces Through a Shared UI Pattern Library

NASA Astrophysics Data System (ADS)

Siarto, J.

2014-12-01

As more Earth science software tools and services move to the web--the design and usability of those tools become ever more important. A good user interface is becoming expected and users are becoming increasingly intolerant of websites and web applications that work against them. The Earthdata UI Pattern Library attempts to give these scientists and developers the design tools they need to make usable, compelling user interfaces without the associated overhead of using a full design team. Patterns are tested and functional user interface elements targeted specifically at the Earth science community and will include web layouts, buttons, tables, typography, iconography, mapping and visualization/graphing widgets. These UI elements have emerged as the result of extensive user testing, research and software development within the NASA Earthdata team over the past year.

A Web 2.0 Interface to Ion Stopping Power and Other Physics Routines for High Energy Density Physics Applications

NASA Astrophysics Data System (ADS)

Stoltz, Peter; Veitzer, Seth

2008-04-01

We present a new Web 2.0-based interface to physics routines for High Energy Density Physics applications. These routines include models for ion stopping power, sputtering, secondary electron yields and energies, impact ionization cross sections, and atomic radiated power. The Web 2.0 interface allows users to easily explore the results of the models before using the routines within other codes or to analyze experimental results. We discuss how we used various Web 2.0 tools, including the Python 2.5, Django, and the Yahoo User Interface library. Finally, we demonstrate the interface by showing as an example the stopping power algorithms researchers are currently using within the Hydra code to analyze warm, dense matter experiments underway at the Neutralized Drift Compression Experiment facility at Lawrence Berkeley National Laboratory.

WebSat ‐ A web software for microsatellite marker development

PubMed Central

Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

An integrated WebGIS framework for volunteered geographic information and social media in soil and water conservation.

PubMed

Werts, Joshua D; Mikhailova, Elena A; Post, Christopher J; Sharp, Julia L

2012-04-01

Volunteered geographic information and social networking in a WebGIS has the potential to increase public participation in soil and water conservation, promote environmental awareness and change, and provide timely data that may be otherwise unavailable to policymakers in soil and water conservation management. The objectives of this study were: (1) to develop a framework for combining current technologies, computing advances, data sources, and social media; and (2) develop and test an online web mapping interface. The mapping interface integrates Microsoft Silverlight, Bing Maps, ArcGIS Server, Google Picasa Web Albums Data API, RSS, Google Analytics, and Facebook to create a rich user experience. The website allows the public to upload photos and attributes of their own subdivisions or sites they have identified and explore other submissions. The website was made available to the public in early February 2011 at http://www.AbandonedDevelopments.com and evaluated for its potential long-term success in a pilot study.

An Integrated WebGIS Framework for Volunteered Geographic Information and Social Media in Soil and Water Conservation

NASA Astrophysics Data System (ADS)

Werts, Joshua D.; Mikhailova, Elena A.; Post, Christopher J.; Sharp, Julia L.

2012-04-01

Volunteered geographic information and social networking in a WebGIS has the potential to increase public participation in soil and water conservation, promote environmental awareness and change, and provide timely data that may be otherwise unavailable to policymakers in soil and water conservation management. The objectives of this study were: (1) to develop a framework for combining current technologies, computing advances, data sources, and social media; and (2) develop and test an online web mapping interface. The mapping interface integrates Microsoft Silverlight, Bing Maps, ArcGIS Server, Google Picasa Web Albums Data API, RSS, Google Analytics, and Facebook to create a rich user experience. The website allows the public to upload photos and attributes of their own subdivisions or sites they have identified and explore other submissions. The website was made available to the public in early February 2011 at http://www.AbandonedDevelopments.com and evaluated for its potential long-term success in a pilot study.

DIANA-microT web server: elucidating microRNA functions through target prediction.

PubMed

Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

2009-07-01

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

Scalable web services for the PSIPRED Protein Analysis Workbench.

PubMed

Buchan, Daniel W A; Minneci, Federico; Nugent, Tim C O; Bryson, Kevin; Jones, David T

2013-07-01

Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

PubMed

Hancock, David; Wilson, Michael; Velarde, Giles; Morrison, Norman; Hayes, Andrew; Hulme, Helen; Wood, A Joseph; Nashar, Karim; Kell, Douglas B; Brass, Andy

2005-11-03

maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

Providing Multi-Page Data Extraction Services with XWRAPComposer

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

Liu, Ling; Zhang, Jianjun; Han, Wei

2008-04-30

Dynamic Web data sources – sometimes known collectively as the Deep Web – increase the utility of the Web by providing intuitive access to data repositories anywhere that Web access is available. Deep Web services provide access to real-time information, like entertainment event listings, or present a Web interface to large databases or other data repositories. Recent studies suggest that the size and growth rate of the dynamic Web greatly exceed that of the static Web, yet dynamic content is often ignored by existing search engine indexers owing to the technical challenges that arise when attempting to search the Deepmore » Web. To address these challenges, we present DYNABOT, a service-centric crawler for discovering and clustering Deep Web sources offering dynamic content. DYNABOT has three unique characteristics. First, DYNABOT utilizes a service class model of the Web implemented through the construction of service class descriptions (SCDs). Second, DYNABOT employs a modular, self-tuning system architecture for focused crawling of the Deep Web using service class descriptions. Third, DYNABOT incorporates methods and algorithms for efficient probing of the Deep Web and for discovering and clustering Deep Web sources and services through SCD-based service matching analysis. Our experimental results demonstrate the effectiveness of the service class discovery, probing, and matching algorithms and suggest techniques for efficiently managing service discovery in the face of the immense scale of the Deep Web.« less

Web Map Services (WMS) Global Mosaic

NASA Technical Reports Server (NTRS)

Percivall, George; Plesea, Lucian

2003-01-01

The WMS Global Mosaic provides access to imagery of the global landmass using an open standard for web mapping. The seamless image is a mosaic of Landsat 7 scenes; geographically-accurate with 30 and 15 meter resolutions. By using the OpenGIS Web Map Service (WMS) interface, any organization can use the global mosaic as a layer in their geospatial applications. Based on a trade study, an implementation approach was chosen that extends a previously developed WMS hosting a Landsat 5 CONUS mosaic developed by JPL. The WMS Global Mosaic supports the NASA Geospatial Interoperability Office goal of providing an integrated digital representation of the Earth, widely accessible for humanity's critical decisions.

A Web interface generator for molecular biology programs in Unix.

PubMed

Letondal, C

2001-01-01

Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration. The program has been used for three years by about 15000 users throughout the world; it has recently been installed on other sites and evaluated as a standard user interface for EMBOSS programs.

DESCQA: Synthetic Sky Catalog Validation Framework

NASA Astrophysics Data System (ADS)

Mao, Yao-Yuan; Uram, Thomas D.; Zhou, Rongpu; Kovacs, Eve; Ricker, Paul M.; Kalmbach, J. Bryce; Padilla, Nelson; Lanusse, François; Zu, Ying; Tenneti, Ananth; Vikraman, Vinu; DeRose, Joseph

2018-04-01

The DESCQA framework provides rigorous validation protocols for assessing the quality of high-quality simulated sky catalogs in a straightforward and comprehensive way. DESCQA enables the inspection, validation, and comparison of an inhomogeneous set of synthetic catalogs via the provision of a common interface within an automated framework. An interactive web interface is also available at portal.nersc.gov/project/lsst/descqa.

Service-oriented model-encapsulation strategy for sharing and integrating heterogeneous geo-analysis models in an open web environment

NASA Astrophysics Data System (ADS)

Yue, Songshan; Chen, Min; Wen, Yongning; Lu, Guonian

2016-04-01

Earth environment is extremely complicated and constantly changing; thus, it is widely accepted that the use of a single geo-analysis model cannot accurately represent all details when solving complex geo-problems. Over several years of research, numerous geo-analysis models have been developed. However, a collaborative barrier between model providers and model users still exists. The development of cloud computing has provided a new and promising approach for sharing and integrating geo-analysis models across an open web environment. To share and integrate these heterogeneous models, encapsulation studies should be conducted that are aimed at shielding original execution differences to create services which can be reused in the web environment. Although some model service standards (such as Web Processing Service (WPS) and Geo Processing Workflow (GPW)) have been designed and developed to help researchers construct model services, various problems regarding model encapsulation remain. (1) The descriptions of geo-analysis models are complicated and typically require rich-text descriptions and case-study illustrations, which are difficult to fully represent within a single web request (such as the GetCapabilities and DescribeProcess operations in the WPS standard). (2) Although Web Service technologies can be used to publish model services, model users who want to use a geo-analysis model and copy the model service into another computer still encounter problems (e.g., they cannot access the model deployment dependencies information). This study presents a strategy for encapsulating geo-analysis models to reduce problems encountered when sharing models between model providers and model users and supports the tasks with different web service standards (e.g., the WPS standard). A description method for heterogeneous geo-analysis models is studied. Based on the model description information, the methods for encapsulating the model-execution program to model services and for describing model-service deployment information are also included in the proposed strategy. Hence, the model-description interface, model-execution interface and model-deployment interface are studied to help model providers and model users more easily share, reuse and integrate geo-analysis models in an open web environment. Finally, a prototype system is established, and the WPS standard is employed as an example to verify the capability and practicability of the model-encapsulation strategy. The results show that it is more convenient for modellers to share and integrate heterogeneous geo-analysis models in cloud computing platforms.

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

NASA Astrophysics Data System (ADS)

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

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

Validating the usability of an interactive Earth Observation based web service for landslide investigation

NASA Astrophysics Data System (ADS)

Albrecht, Florian; Weinke, Elisabeth; Eisank, Clemens; Vecchiotti, Filippo; Hölbling, Daniel; Friedl, Barbara; Kociu, Arben

2017-04-01

Regional authorities and infrastructure maintainers in almost all mountainous regions of the Earth need detailed and up-to-date landslide inventories for hazard and risk management. Landslide inventories usually are compiled through ground surveys and manual image interpretation following landslide triggering events. We developed a web service that uses Earth Observation (EO) data to support the mapping and monitoring tasks for improving the collection of landslide information. The planned validation of the EO-based web service does not only cover the analysis of the achievable landslide information quality but also the usability and user friendliness of the user interface. The underlying validation criteria are based on the user requirements and the defined tasks and aims in the work description of the FFG project Land@Slide (EO-based landslide mapping: from methodological developments to automated web-based information delivery). The service will be validated in collaboration with stakeholders, decision makers and experts. Users are requested to test the web service functionality and give feedback with a web-based questionnaire by following the subsequently described workflow. The users will operate the web-service via the responsive user interface and can extract landslide information from EO data. They compare it to reference data for quality assessment, for monitoring changes and for assessing landslide-affected infrastructure. An overview page lets the user explore a list of example projects with resulting landslide maps and mapping workflow descriptions. The example projects include mapped landslides in several test areas in Austria and Northern Italy. Landslides were extracted from high resolution (HR) and very high resolution (VHR) satellite imagery, such as Landsat, Sentinel-2, SPOT-5, WorldView-2/3 or Pléiades. The user can create his/her own project by selecting available satellite imagery or by uploading new data. Subsequently, a new landslide extraction workflow can be initiated through the functionality that the web service provides: (1) a segmentation of the image into spectrally homogeneous objects, (2) a classification of the objects into landslide and non-landslide areas and (3) an editing tool for the manual refinement of extracted landslide boundaries. In addition, the user interface of the web service provides tools that enable the user (4) to perform a monitoring that identifies changes between landslide maps of different points in time, (5) to perform a validation of the landslide maps by comparing them to reference data, and (6) to perform an assessment of affected infrastructure by comparing the landslide maps to respective infrastructure data. After exploring the web service functionality, the users are asked to fill in the online validation protocol in form of a questionnaire in order to provide their feedback. Concerning usability, we evaluate how intuitive the web service functionality can be operated, how well the integrated help information guides the users, and what kind of background information, e.g. remote sensing concepts and theory, is necessary for a practitioner to fully exploit the value of EO data. The feedback will be used for improving the user interface and for the implementation of additional functionality.

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.

PubMed

Basu, M K

2001-06-01

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

Program Management Tool

NASA Technical Reports Server (NTRS)

Gawadiak, Yuri; Wong, Alan; Maluf, David; Bell, David; Gurram, Mohana; Tran, Khai Peter; Hsu, Jennifer; Yagi, Kenji; Patel, Hemil

2007-01-01

The Program Management Tool (PMT) is a comprehensive, Web-enabled business intelligence software tool for assisting program and project managers within NASA enterprises in gathering, comprehending, and disseminating information on the progress of their programs and projects. The PMT provides planning and management support for implementing NASA programmatic and project management processes and requirements. It provides an online environment for program and line management to develop, communicate, and manage their programs, projects, and tasks in a comprehensive tool suite. The information managed by use of the PMT can include monthly reports as well as data on goals, deliverables, milestones, business processes, personnel, task plans, monthly reports, and budgetary allocations. The PMT provides an intuitive and enhanced Web interface to automate the tedious process of gathering and sharing monthly progress reports, task plans, financial data, and other information on project resources based on technical, schedule, budget, and management criteria and merits. The PMT is consistent with the latest Web standards and software practices, including the use of Extensible Markup Language (XML) for exchanging data and the WebDAV (Web Distributed Authoring and Versioning) protocol for collaborative management of documents. The PMT provides graphical displays of resource allocations in the form of bar and pie charts using Microsoft Excel Visual Basic for Application (VBA) libraries. The PMT has an extensible architecture that enables integration of PMT with other strategic-information software systems, including, for example, the Erasmus reporting system, now part of the NASA Integrated Enterprise Management Program (IEMP) tool suite, at NASA Marshall Space Flight Center (MSFC). The PMT data architecture provides automated and extensive software interfaces and reports to various strategic information systems to eliminate duplicative human entries and minimize data integrity issues among various NASA systems that impact schedules and planning.

FERMI/GLAST Integrated Trending and Plotting System Release 5.0

NASA Technical Reports Server (NTRS)

Ritter, Sheila; Brumer, Haim; Reitan, Denise

2012-01-01

An Integrated Trending and Plotting System (ITPS) is a trending, analysis, and plotting system used by space missions to determine performance and status of spacecraft and its instruments. ITPS supports several NASA mission operational control centers providing engineers, ground controllers, and scientists with access to the entire spacecraft telemetry data archive for the life of the mission, and includes a secure Web component for remote access. FERMI/GLAST ITPS Release 5.0 features include the option to display dates (yyyy/ddd) instead of orbit numbers along orbital Long-Term Trend (LTT) plot axis, the ability to save statistics from daily production plots as image files, and removal of redundant edit/create Input Definition File (IDF) screens. Other features are a fix to address invalid packet lengths, a change in naming convention of image files in order to use in script, the ability to save all ITPS plot images (from Windows or the Web) as GIF or PNG format, the ability to specify ymin and ymax on plots where previously only the desired range could be specified, Web interface capability to plot IDFs that contain out-oforder page and plot numbers, and a fix to change all default file names to show yyyydddhhmmss time stamps instead of hhmmssdddyyyy. A Web interface capability sorts files based on modification date (with newest one at top), and the statistics block can be displayed via a Web interface. Via the Web, users can graphically view the volume of telemetry data from each day contained in the ITPS archive in the Web digest. The ITPS could be also used in nonspace fields that need to plot data or trend data, including financial and banking systems, aviation and transportation systems, healthcare and educational systems, sales and marketing, and housing and construction.

Software architecture and design of the web services facilitating climate model diagnostic analysis

NASA Astrophysics Data System (ADS)

Pan, L.; Lee, S.; Zhang, J.; Tang, B.; Zhai, C.; Jiang, J. H.; Wang, W.; Bao, Q.; Qi, M.; Kubar, T. L.; Teixeira, J.

2015-12-01

Climate model diagnostic analysis is a computationally- and data-intensive task because it involves multiple numerical model outputs and satellite observation data that can both be high resolution. We have built an online tool that facilitates this process. The tool is called Climate Model Diagnostic Analyzer (CMDA). It employs the web service technology and provides a web-based user interface. The benefits of these choices include: (1) No installation of any software other than a browser, hence it is platform compatable; (2) Co-location of computation and big data on the server side, and small results and plots to be downloaded on the client side, hence high data efficiency; (3) multi-threaded implementation to achieve parallel performance on multi-core servers; and (4) cloud deployment so each user has a dedicated virtual machine. In this presentation, we will focus on the computer science aspects of this tool, namely the architectural design, the infrastructure of the web services, the implementation of the web-based user interface, the mechanism of provenance collection, the approach to virtualization, and the Amazon Cloud deployment. As an example, We will describe our methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). Another example is the use of Docker, a light-weight virtualization container, to distribute and deploy CMDA onto an Amazon EC2 instance. Our tool of CMDA has been successfully used in the 2014 Summer School hosted by the JPL Center for Climate Science. Students had positive feedbacks in general and we will report their comments. An enhanced version of CMDA with several new features, some requested by the 2014 students, will be used in the 2015 Summer School soon.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

A Smart Modeling Framework for Integrating BMI-enabled Models as Web Services

NASA Astrophysics Data System (ADS)

Jiang, P.; Elag, M.; Kumar, P.; Peckham, S. D.; Liu, R.; Marini, L.; Hsu, L.

2015-12-01

Serviced-oriented computing provides an opportunity to couple web service models using semantic web technology. Through this approach, models that are exposed as web services can be conserved in their own local environment, thus making it easy for modelers to maintain and update the models. In integrated modeling, the serviced-oriented loose-coupling approach requires (1) a set of models as web services, (2) the model metadata describing the external features of a model (e.g., variable name, unit, computational grid, etc.) and (3) a model integration framework. We present the architecture of coupling web service models that are self-describing by utilizing a smart modeling framework. We expose models that are encapsulated with CSDMS (Community Surface Dynamics Modeling System) Basic Model Interfaces (BMI) as web services. The BMI-enabled models are self-describing by uncovering models' metadata through BMI functions. After a BMI-enabled model is serviced, a client can initialize, execute and retrieve the meta-information of the model by calling its BMI functions over the web. Furthermore, a revised version of EMELI (Peckham, 2015), an Experimental Modeling Environment for Linking and Interoperability, is chosen as the framework for coupling BMI-enabled web service models. EMELI allows users to combine a set of component models into a complex model by standardizing model interface using BMI as well as providing a set of utilities smoothing the integration process (e.g., temporal interpolation). We modify the original EMELI so that the revised modeling framework is able to initialize, execute and find the dependencies of the BMI-enabled web service models. By using the revised EMELI, an example will be presented on integrating a set of topoflow model components that are BMI-enabled and exposed as web services. Reference: Peckham, S.D. (2014) EMELI 1.0: An experimental smart modeling framework for automatic coupling of self-describing models, Proceedings of HIC 2014, 11th International Conf. on Hydroinformatics, New York, NY.

Tools for Integrating Data Access from the IRIS DMC into Research Workflows

NASA Astrophysics Data System (ADS)

Reyes, C. G.; Suleiman, Y. Y.; Trabant, C.; Karstens, R.; Weertman, B. R.

2012-12-01

Web service interfaces at the IRIS Data Management Center (DMC) provide access to a vast archive of seismological and related geophysical data. These interfaces are designed to easily incorporate data access into data processing workflows. Examples of data that may be accessed include: time series data, related metadata, and earthquake information. The DMC has developed command line scripts, MATLAB® interfaces and a Java library to support a wide variety of data access needs. Users of these interfaces do not need to concern themselves with web service details, networking, or even (in most cases) data conversion. Fetch scripts allow access to the DMC archive and are a comfortable fit for command line users. These scripts are written in Perl and are well suited for automation and integration into existing workflows on most operating systems. For metdata and event information, the Fetch scripts even parse the returned data into simple text summaries. The IRIS Java Web Services Library (IRIS-WS Library) allows Java developers the ability to create programs that access the DMC archives seamlessly. By returning the data and information as native Java objects the Library insulates the developer from data formats, network programming and web service details. The MATLAB interfaces leverage this library to allow users access to the DMC archive directly from within MATLAB (r2009b or newer), returning data into variables for immediate use. Data users and research groups are developing other toolkits that use the DMC's web services. Notably, the ObsPy framework developed at LMU Munich is a Python Toolbox that allows seamless access to data and information via the DMC services. Another example is the MATLAB-based GISMO and Waveform Suite developments that can now access data via web services. In summary, there now exist a host of ways that researchers can bring IRIS DMC data directly into their workflows. MATLAB users can use irisFetch.m, command line users can use the various Fetch scripts, Java users can use the IRIS-WS library, and Python users may request data through ObsPy. To learn more about any of these clients see http://www.iris.edu/ws/wsclients/.

Automatic geospatial information Web service composition based on ontology interface matching

NASA Astrophysics Data System (ADS)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

With Web services technology the functions of WebGIS can be presented as a kind of geospatial information service, and helped to overcome the limitation of the information-isolated situation in geospatial information sharing field. Thus Geospatial Information Web service composition, which conglomerates outsourced services working in tandem to offer value-added service, plays the key role in fully taking advantage of geospatial information services. This paper proposes an automatic geospatial information web service composition algorithm that employed the ontology dictionary WordNet to analyze semantic distances among the interfaces. Through making matching between input/output parameters and the semantic meaning of pairs of service interfaces, a geospatial information web service chain can be created from a number of candidate services. A practice of the algorithm is also proposed and the result of it shows the feasibility of this algorithm and the great promise in the emerging demand for geospatial information web service composition.

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)

Migration of the ATLAS Metadata Interface (AMI) to Web 2.0 and cloud

NASA Astrophysics Data System (ADS)

Odier, J.; Albrand, S.; Fulachier, J.; Lambert, F.

2015-12-01

The ATLAS Metadata Interface (AMI), a mature application of more than 10 years of existence, is currently under adaptation to some recently available technologies. The web interfaces, which previously manipulated XML documents using XSL transformations, are being migrated to Asynchronous JavaScript (AJAX). Web development is considerably simplified by the introduction of a framework based on JQuery and Twitter Bootstrap. Finally, the AMI services are being migrated to an OpenStack cloud infrastructure.

UManSysProp v1.0: an online and open-source facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, David; Barley, Mark; Bane, Michael K.; Higham, Nicholas; Aumont, Bernard; Dingle, Nicholas; McFiggans, Gordon

2016-03-01

In this paper we describe the development and application of a new web-based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include pure component vapour pressures, critical properties, and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN (cloud condensation nuclei) activation potential of mixed inorganic-organic aerosol particles; and absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES (Simplified Molecular Input Line Entry System) strings and UManSysProp will automatically extract the relevant information for calculations. Built using open-source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web interface, or can be accessed using the user's own code via a JSON API (application program interface). We also provide the source code for all predictive techniques provided on the site, covered by the GNU GPL (General Public License) license to encourage development of a user community. We have released this via a Github repository (doi:10.5281/zenodo.45143). In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

Making large amounts of meteorological plots easily accessible to users

NASA Astrophysics Data System (ADS)

Lamy-Thepaut, Sylvie; Siemen, Stephan; Sahin, Cihan; Raoult, Baudouin

2015-04-01

The European Centre for Medium-Range Weather Forecasts (ECMWF) is an international organisation providing its member organisations with forecasts in the medium time range of 3 to 15 days, and some longer-range forecasts for up to a year ahead, with varying degrees of detail. As part of its mission, ECMWF generates an increasing number of forecast data products for its users. To support the work of forecasters and researchers and to let them make best use of ECMWF forecasts, the Centre also provides tools and interfaces to visualise their products. This allows users to make use of and explore forecasts without having to transfer large amounts of raw data. This is especially true for products based on ECMWF's 50 member ensemble forecast, where some specific processing and visualisation are applied to extract information. Every day, thousands of raw data are being pushed to the ECMWF's interactive web charts application called ecCharts, and thousands of products are processed and pushed to ECMWF's institutional web site ecCharts provides a highly interactive application to display and manipulate recent numerical forecasts to forecasters in national weather services and ECMWF's commercial customers. With ecCharts forecasters are able to explore ECMWF's medium-range forecasts in far greater detail than has previously been possible on the web, and this as soon as the forecast becomes available. All ecCharts's products are also available through a machine-to-machine web map service based on the OGC Web Map Service (WMS) standard. ECMWF institutional web site provides access to a large number of graphical products. It was entirely redesigned last year. It now shares the same infrastructure as ECMWF's ecCharts, and can benefit of some ecCharts functionalities, for example the dashboard. The dashboard initially developed for ecCharts allows users to organise their own collection of products depending on their work flow, and is being further developed. In its first implementation, It presents the user's products in a single interface with fast access to the original product, and possibilities of synchronous animations between them. But its functionalities are being extended to give users the freedom to collect not only ecCharts's 2D maps and graphs, but also other ECMWF Web products such as monthly and seasonal products, scores, and observation monitoring. The dashboard will play a key role to help the user to interpret the large amount of information that ECMWF is providing. This talk will present examples of how the new user interface can organise complex meteorological maps and graphs and show the new possibilities users have gained by using the web as a medium.

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Nuclear data made easily accessible through the Notre Dame Nuclear Database

NASA Astrophysics Data System (ADS)

Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

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.

SCHeMA web-based observation data information system

NASA Astrophysics Data System (ADS)

Novellino, Antonio; Benedetti, Giacomo; D'Angelo, Paolo; Confalonieri, Fabio; Massa, Francesco; Povero, Paolo; Tercier-Waeber, Marie-Louise

2016-04-01

It is well recognized that the need of sharing ocean data among non-specialized users is constantly increasing. Initiatives that are built upon international standards will contribute to simplify data processing and dissemination, improve user-accessibility also through web browsers, facilitate the sharing of information across the integrated network of ocean observing systems; and ultimately provide a better understanding of the ocean functioning. The SCHeMA (Integrated in Situ Chemical MApping probe) Project is developing an open and modular sensing solution for autonomous in situ high resolution mapping of a wide range of anthropogenic and natural chemical compounds coupled to master bio-physicochemical parameters (www.schema-ocean.eu). The SCHeMA web system is designed to ensure user-friendly data discovery, access and download as well as interoperability with other projects through a dedicated interface that implements the Global Earth Observation System of Systems - Common Infrastructure (GCI) recommendations and the international Open Geospatial Consortium - Sensor Web Enablement (OGC-SWE) standards. This approach will insure data accessibility in compliance with major European Directives and recommendations. Being modular, the system allows the plug-and-play of commercially available probes as well as new sensor probess under development within the project. The access to the network of monitoring probes is provided via a web-based system interface that, being implemented as a SOS (Sensor Observation Service), is providing standard interoperability and access tosensor observations systems through O&M standard - as well as sensor descriptions - encoded in Sensor Model Language (SensorML). The use of common vocabularies in all metadatabases and data formats, to describe data in an already harmonized and common standard is a prerequisite towards consistency and interoperability. Therefore, the SCHeMA SOS has adopted the SeaVox common vocabularies populated by SeaDataNet network of National Oceanographic Data Centres. The SCHeMA presentation layer, a fundamental part of the software architecture, offers to the user a bidirectional interaction with the integrated system allowing to manage and configure the sensor probes; view the stored observations and metadata, and handle alarms. The overall structure of the web portal developed within the SCHeMA initiative (Sensor Configuration, development of Core Profile interface for data access via OGC standard, external services such as web services, WMS, WFS; and Data download and query manager) will be presented and illustrated with examples of ongoing tests in costal and open sea.

MaROS Strategic Relay Planning and Coordination Interfaces

NASA Technical Reports Server (NTRS)

Allard, Daniel A.

2010-01-01

The Mars Relay Operations Service (MaROS) is designed to provide planning and analysis tools in support of ongoing Mars Network relay operations. Strategic relay planning requires coordination between lander and orbiter mission ground data system (GDS) teams to schedule and execute relay communications passes. MaROS centralizes this process, correlating all data relevant to relay coordination to provide a cohesive picture of the relay state. Service users interact with the system through thin-layer command line and web user interface client applications. Users provide and utilize data such as lander view periods of orbiters, Deep Space Network (DSN) antenna tracks, and reports of relay pass performance. Users upload and download relevant relay data via formally defined and documented file structures including some described in Extensible Markup Language (XML). Clients interface with the system via an http-based Representational State Transfer (ReST) pattern using Javascript Object Notation (JSON) formats. This paper will provide a general overview of the service architecture and detail the software interfaces and considerations for interface design.

The climate4impact platform: Providing, tailoring and facilitating climate model data access

NASA Astrophysics Data System (ADS)

Pagé, Christian; Pagani, Andrea; Plieger, Maarten; Som de Cerff, Wim; Mihajlovski, Andrej; de Vreede, Ernst; Spinuso, Alessandro; Hutjes, Ronald; de Jong, Fokke; Bärring, Lars; Vega, Manuel; Cofiño, Antonio; d'Anca, Alessandro; Fiore, Sandro; Kolax, Michael

2017-04-01

One of the main objectives of climate4impact is to provide standardized web services and tools that are reusable in other portals. These services include web processing services, web coverage services and web mapping services (WPS, WCS and WMS). Tailored portals can be targeted to specific communities and/or countries/regions while making use of those services. Easier access to climate data is very important for the climate change impact communities. To fulfill this objective, the climate4impact (http://climate4impact.eu/) web portal and services has been developed, targeting climate change impact modellers, impact and adaptation consultants, as well as other experts using climate change data. It provides to users harmonized access to climate model data through tailored services. It features static and dynamic documentation, Use Cases and best practice examples, an advanced search interface, an integrated authentication and authorization system with the Earth System Grid Federation (ESGF), a visualization interface with ADAGUC web mapping tools. In the latest version, statistical downscaling services, provided by the Santander Meteorology Group Downscaling Portal, were integrated. An innovative interface to integrate statistical downscaling services will be released in the upcoming version. The latter will be a big step in bridging the gap between climate scientists and the climate change impact communities. The climate4impact portal builds on the infrastructure of an international distributed database that has been set to disseminate the results from the global climate model results of the Coupled Model Intercomparison project Phase 5 (CMIP5). This database, the ESGF, is an international collaboration that develops, deploys and maintains software infrastructure for the management, dissemination, and analysis of climate model data. The European FP7 project IS-ENES, Infrastructure for the European Network for Earth System modelling, supports the European contribution to ESGF and contributes to the ESGF open source effort, notably through the development of search, monitoring, quality control, and metadata services. In its second phase, IS-ENES2 supports the implementation of regional climate model results from the international Coordinated Regional Downscaling Experiments (CORDEX). These services were extended within the European FP7 Climate Information Portal for Copernicus (CLIPC) project, and some could be later integrated into the European Copernicus platform.

Developing a smartphone interface for the Florida Environmental Public Health Tracking Web portal.

PubMed

Jordan, Melissa; DuClos, Chris; Folsom, John; Thomas, Rebecca

2015-01-01

As smartphone and tablet devices continue to proliferate, it is becoming increasingly important to tailor information delivery to the mobile device. The Florida Environmental Public Health Tracking Program recognized that the mobile device user needs Web content formatted to smaller screen sizes, simplified data displays, and reduced textual information. The Florida Environmental Public Health Tracking Program developed a smartphone-friendly version of the state Web portal for easier access by mobile device users. The resulting smartphone-friendly portal combines calculated data measures such as inpatient hospitalizations and emergency department visits and presents them grouped by county, along with temporal trend graphs. An abbreviated version of the public health messaging provided on the traditional Web portal is also provided, along with social media connections. As a result of these efforts, the percentage of Web site visitors using an iPhone tripled in just 1 year.

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

AMPA: an automated web server for prediction of protein antimicrobial regions.

PubMed

Torrent, Marc; Di Tommaso, Paolo; Pulido, David; Nogués, M Victòria; Notredame, Cedric; Boix, Ester; Andreu, David

2012-01-01

AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination. AMPA is freely available on the web at http://tcoffee.crg.cat/apps/ampa. The source code is also available in the web. marc.torrent@upf.edu; david.andreu@upf.edu Supplementary data are available at Bioinformatics online.

BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns.

PubMed

Wei, Qing; La, David; Kihara, Daisuke

2017-01-01

Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods. BindML predicts protein-protein interaction sites by identifying mutation patterns found in known protein-protein complexes using phylogenetic substitution models. BindML+ is an extension of BindML for distinguishing permanent and transient types of protein-protein interaction sites. We developed an interactive web-server that provides a convenient interface to assist in structural visualization of protein-protein interactions site predictions. The input data for the web-server are a tertiary structure of interest. BindML and BindML+ are available at http://kiharalab.org/bindml/ and http://kiharalab.org/bindml/plus/ .

A Web Service and Interface for Remote Electronic Device Characterization

ERIC Educational Resources Information Center

Dutta, S.; Prakash, S.; Estrada, D.; Pop, E.

2011-01-01

A lightweight Web Service and a Web site interface have been developed, which enable remote measurements of electronic devices as a "virtual laboratory" for undergraduate engineering classes. Using standard browsers without additional plugins (such as Internet Explorer, Firefox, or even Safari on an iPhone), remote users can control a Keithley…

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study.

PubMed

Lizarraga, Gabriel; Li, Chunfei; Cabrerizo, Mercedes; Barker, Warren; Loewenstein, David A; Duara, Ranjan; Adjouadi, Malek

2018-04-26

Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. ©Gabriel Lizarraga, Chunfei Li, Mercedes Cabrerizo, Warren Barker, David A Loewenstein, Ranjan Duara, Malek Adjouadi. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 26.04.2018.

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

PubMed Central

Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

2014-01-01

The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881

STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

PubMed Central

Neshich, Goran; Togawa, Roberto C.; Mancini, Adauto L.; Kuser, Paula R.; Yamagishi, Michel E. B.; Pappas, Georgios; Torres, Wellington V.; Campos, Tharsis Fonseca e; Ferreira, Leonardo L.; Luna, Fabio M.; Oliveira, Adilton G.; Miura, Ronald T.; Inoue, Marcus K.; Horita, Luiz G.; de Souza, Dimas F.; Dominiquini, Fabiana; Álvaro, Alexandre; Lima, Cleber S.; Ogawa, Fabio O.; Gomes, Gabriel B.; Palandrani, Juliana F.; dos Santos, Gabriela F.; de Freitas, Esther M.; Mattiuz, Amanda R.; Costa, Ivan C.; de Almeida, Celso L.; Souza, Savio; Baudet, Christian; Higa, Roberto H.

2003-01-01

STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Cα–Cα and Cβ–Cβ distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)—amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS. PMID:12824333

IFIS Model-Plus: A Web-Based GUI for Visualization, Comparison and Evaluation of Distributed Flood Forecasts and Hindcasts

NASA Astrophysics Data System (ADS)

Krajewski, W. F.; Della Libera Zanchetta, A.; Mantilla, R.; Demir, I.

2017-12-01

This work explores the use of hydroinformatics tools to provide an user friendly and accessible interface for executing and assessing the output of realtime flood forecasts using distributed hydrological models. The main result is the implementation of a web system that uses an Iowa Flood Information System (IFIS)-based environment for graphical displays of rainfall-runoff simulation results for both real-time and past storm events. It communicates with ASYNCH ODE solver to perform large-scale distributed hydrological modeling based on segmentation of the terrain into hillslope-link hydrologic units. The cyber-platform also allows hindcast of model performance by testing multiple model configurations and assumptions of vertical flows in the soils. The scope of the currently implemented system is the entire set of contributing watersheds for the territory of the state of Iowa. The interface provides resources for visualization of animated maps for different water-related modeled states of the environment, including flood-waves propagation with classification of flood magnitude, runoff generation, surface soil moisture and total water column in the soil. Additional tools for comparing different model configurations and performing model evaluation by comparing to observed variables at monitored sites are also available. The user friendly interface has been published to the web under the URL http://ifis.iowafloodcenter.org/ifis/sc/modelplus/.

mySyntenyPortal: an application package to construct websites for synteny block analysis.

PubMed

Lee, Jongin; Lee, Daehwan; Sim, Mikang; Kwon, Daehong; Kim, Juyeon; Ko, Younhee; Kim, Jaebum

2018-06-05

Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users' own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user's own genome data.

Modern Technologies aspects for Oceanographic Data Management and Dissemination : The HNODC Implementation

NASA Astrophysics Data System (ADS)

Lykiardopoulos, A.; Iona, A.; Lakes, V.; Batis, A.; Balopoulos, E.

2009-04-01

The development of new technologies for the aim of enhancing Web Applications with Dynamically data access was the starting point for Geospatial Web Applications to developed at the same time as well. By the means of these technologies the Web Applications embed the capability of presenting Geographical representations of the Geo Information. The induction in nowadays, of the state of the art technologies known as Web Services, enforce the Web Applications to have interoperability among them i.e. to be able to process requests from each other via a network. In particular throughout the Oceanographic Community, modern Geographical Information systems based on Geospatial Web Services are now developed or will be developed shortly in the near future, with capabilities of managing the information itself fully through Web Based Geographical Interfaces. The exploitation of HNODC Data Base, through a Web Based Application enhanced with Web Services by the use of open source tolls may be consider as an ideal case of such implementation. Hellenic National Oceanographic Data Center (HNODC) as a National Public Oceanographic Data provider and at the same time a member of the International Net of Oceanographic Data Centers( IOC/IODE), owns a very big volume of Data and Relevant information about the Marine Ecosystem. For the efficient management and exploitation of these Data, a relational Data Base has been constructed with a storage of over 300.000 station data concerning, physical, chemical and biological Oceanographic information. The development of a modern Web Application for the End User worldwide to be able to explore and navigate throughout HNODC data via the use of an interface with the capability of presenting Geographical representations of the Geo Information, is today a fact. The application is constituted with State of the art software components and tools such as: • Geospatial and no Spatial Web Services mechanisms • Geospatial open source tools for the creation of Dynamic Geographical Representations. • Communication protocols (messaging mechanisms) in all Layers such as XML and GML together with SOAP protocol via Apache/Axis. At the same time the application may interact with any other SOA application either in sending or receiving Geospatial Data through Geographical Layers, since it inherits the big advantage of interoperability between Web Services systems. Roughly the Architecture can denoted as follows: • At the back End Open source PostgreSQL DBMS stands as the data storage mechanism with more than one Data Base Schemas cause of the separation of the Geospatial Data and the non Geospatial Data. • UMN Map Server and Geoserver are the mechanisms for: Represent Geospatial Data via Web Map Service (WMS) Querying and Navigating in Geospatial and Meta Data Information via Web Feature Service (WFS) oAnd in the near future Transacting and processing new or existing Geospatial Data via Web Processing Service (WPS) • Map Bender, a geospatial portal site management software for OGC and OWS architectures acts as the integration module between the Geospatial Mechanisms. Mapbender comes with an embedded data model capable to manage interfaces for displaying, navigating and querying OGC compliant web map and feature services (WMS and transactional WFS). • Apache and Tomcat stand again as the Web Service middle Layers • Apache Axis with it's embedded implementation of the SOAP protocol ("Simple Object Access Protocol") acts as the No spatial data Mechanism of Web Services. These modules of the platform are still under development but their implementation will be fulfilled in the near future. • And a new Web user Interface for the end user based on enhanced and customized version of a MapBender GUI, a powerful Web Services client. For HNODC the interoperability of Web Services is the big advantage of the developed platform since it is capable to act in the future as provider and consumer of Web Services in both ways: • Either as data products provider for external SOA platforms. • Or as consumer of data products from external SOA platforms for new applications to be developed or for existing applications to be enhanced. A great paradigm of Data Managenet integration and dissemination via the use of such technologies is the European's Union Research Project Seadatanet, with the main objective to develop a standardized distributed system for managing and disseminating the large and diverse data sets and to enhance the currently existing infrastructures with Web Services Further more and when the technology of Web Processing Service (WPS), will be mature enough and applicable for development, the derived data products will be able to have any kind of GIS functionality for consumers across the network. From this point of view HNODC, joins the global scientific community by providing and consuming application Independent data products.

A performance study of WebDav access to storages within the Belle II collaboration

NASA Astrophysics Data System (ADS)

Pardi, S.; Russo, G.

2017-10-01

WebDav and HTTP are becoming popular protocols for data access in the High Energy Physics community. The most used Grid and Cloud storage solutions provide such kind of interfaces, in this scenario tuning and performance evaluation became crucial aspects to promote the adoption of these protocols within the Belle II community. In this work, we present the results of a large-scale test activity, made with the goal to evaluate performances and reliability of the WebDav protocol, and study a possible adoption for the user analysis. More specifically, we considered a pilot infrastructure composed by a set of storage elements configured with the WebDav interface, hosted at the Belle II sites. The performance tests include a comparison with xrootd and gridftp. As reference tests we used a set of analysis jobs running under the Belle II software framework, accessing the input data with the ROOT I/O library, in order to simulate as much as possible a realistic user activity. The final analysis shows the possibility to achieve promising performances with WebDav on different storage systems, and gives an interesting feedback, for Belle II community and for other high energy physics experiments.

Development of a 3D WebGIS System for Retrieving and Visualizing CityGML Data Based on their Geometric and Semantic Characteristics by Using Free and Open Source Technology

NASA Astrophysics Data System (ADS)

Pispidikis, I.; Dimopoulou, E.

2016-10-01

CityGML is considered as an optimal standard for representing 3D city models. However, international experience has shown that visualization of the latter is quite difficult to be implemented on the web, due to the large size of data and the complexity of CityGML. As a result, in the context of this paper, a 3D WebGIS application is developed in order to successfully retrieve and visualize CityGML data in accordance with their respective geometric and semantic characteristics. Furthermore, the available web technologies and the architecture of WebGIS systems are investigated, as provided by international experience, in order to be utilized in the most appropriate way for the purposes of this paper. Specifically, a PostgreSQL/ PostGIS Database is used, in compliance with the 3DCityDB schema. At Server tier, Apache HTTP Server and GeoServer are utilized, while a Server Side programming language PHP is used. At Client tier, which implemented the interface of the application, the following technologies were used: JQuery, AJAX, JavaScript, HTML5, WebGL and Ol3-Cesium. Finally, it is worth mentioning that the application's primary objectives are a user-friendly interface and a fully open source development.

LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis.

PubMed

Zheng, Jie; Erzurumluoglu, A Mesut; Elsworth, Benjamin L; Kemp, John P; Howe, Laurence; Haycock, Philip C; Hemani, Gibran; Tansey, Katherine; Laurin, Charles; Pourcain, Beate St; Warrington, Nicole M; Finucane, Hilary K; Price, Alkes L; Bulik-Sullivan, Brendan K; Anttila, Verneri; Paternoster, Lavinia; Gaunt, Tom R; Evans, David M; Neale, Benjamin M

2017-01-15

LD score regression is a reliable and efficient method of using genome-wide association study (GWAS) summary-level results data to estimate the SNP heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. Because the method relies on summary level results data, LD score regression is computationally tractable even for very large sample sizes. However, publicly available GWAS summary-level data are typically stored in different databases and have different formats, making it difficult to apply LD score regression to estimate genetic correlations across many different traits simultaneously. In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the LD score regression analysis pipeline. To demonstrate functionality and validate our software, we replicated previously reported LD score regression analyses of 49 traits/diseases using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes. We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits. In response to the growing availability of publicly accessible GWAS summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies. The web interface and instructions for using LD Hub are available at http://ldsc.broadinstitute.org/ CONTACT: jie.zheng@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Applying Sensor Web Technology to Marine Sensor Data

NASA Astrophysics Data System (ADS)

Jirka, Simon; del Rio, Joaquin; Mihai Toma, Daniel; Nüst, Daniel; Stasch, Christoph; Delory, Eric

2015-04-01

In this contribution we present two activities illustrating how Sensor Web technology helps to enable a flexible and interoperable sharing of marine observation data based on standards. An important foundation is the Sensor Web Architecture developed by the European FP7 project NeXOS (Next generation Low-Cost Multifunctional Web Enabled Ocean Sensor Systems Empowering Marine, Maritime and Fisheries Management). This architecture relies on the Open Geospatial Consortium's (OGC) Sensor Web Enablement (SWE) framework. It is an exemplary solution for facilitating the interoperable exchange of marine observation data within and between (research) organisations. The architecture addresses a series of functional and non-functional requirements which are fulfilled through different types of OGC SWE components. The diverse functionalities offered by the NeXOS Sensor Web architecture are shown in the following overview: - Pull-based observation data download: This is achieved through the OGC Sensor Observation Service (SOS) 2.0 interface standard. - Push-based delivery of observation data to allow users the subscription to new measurements that are relevant for them: For this purpose there are currently several specification activities under evaluation (e.g. OGC Sensor Event Service, OGC Publish/Subscribe Standards Working Group). - (Web-based) visualisation of marine observation data: Implemented through SOS client applications. - Configuration and controlling of sensor devices: This is ensured through the OGC Sensor Planning Service 2.0 interface. - Bridging between sensors/data loggers and Sensor Web components: For this purpose several components such as the "Smart Electronic Interface for Sensor Interoperability" (SEISI) concept are developed; this is complemented by a more lightweight SOS extension (e.g. based on the W3C Efficient XML Interchange (EXI) format). To further advance this architecture, there is on-going work to develop dedicated profiles of selected OGC SWE specifications that provide stricter guidance how these standards shall be applied to marine data (e.g. SensorML 2.0 profiles stating which metadata elements are mandatory building upon the ESONET Sensor Registry developments, etc.). Within the NeXOS project the presented architecture is implemented as a set of open source components. These implementations can be re-used by all interested scientists and data providers needing tools for publishing or consuming oceanographic sensor data. In further projects such as the European project FixO3 (Fixed-point Open Ocean Observatories), these software development activities are complemented with additional efforts to provide guidance how Sensor Web technology can be applied in an efficient manner. This way, not only software components are made available but also documentation and information resources that help to understand which types of Sensor Web deployments are best suited to fulfil different types of user requirements.

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.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

A User-centered Model for Web Site Design

PubMed Central

Kinzie, Mable B.; Cohn, Wendy F.; Julian, Marti F.; Knaus, William A.

2002-01-01

As the Internet continues to grow as a delivery medium for health information, the design of effective Web sites becomes increasingly important. In this paper, the authors provide an overview of one effective model for Web site design, a user-centered process that includes techniques for needs assessment, goal/task analysis, user interface design, and rapid prototyping. They detail how this approach was employed to design a family health history Web site, Health Heritage . This Web site helps patients record and maintain their family health histories in a secure, confidential manner. It also supports primary care physicians through analysis of health histories, identification of potential risks, and provision of health care recommendations. Visual examples of the design process are provided to show how the use of this model resulted in an easy-to-use Web site that is likely to meet user needs. The model is effective across diverse content arenas and is appropriate for applications in varied media. PMID:12087113

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches

PubMed Central

Romer, Katherine A.; Kayombya, Guy-Richard; Fraenkel, Ernest

2007-01-01

WebMOTIFS provides a web interface that facilitates the discovery and analysis of DNA-sequence motifs. Several studies have shown that the accuracy of motif discovery can be significantly improved by using multiple de novo motif discovery programs and using randomized control calculations to identify the most significant motifs or by using Bayesian approaches. WebMOTIFS makes it easy to apply these strategies. Using a single submission form, users can run several motif discovery programs and score, cluster and visualize the results. In addition, the Bayesian motif discovery program THEME can be used to determine the class of transcription factors that is most likely to regulate a set of sequences. Input can be provided as a list of gene or probe identifiers. Used with the default settings, WebMOTIFS accurately identifies biologically relevant motifs from diverse data in several species. WebMOTIFS is freely available at http://fraenkel.mit.edu/webmotifs. PMID:17584794

The impact of web services at the IRIS DMC

NASA Astrophysics Data System (ADS)

Weekly, R. T.; Trabant, C. M.; Ahern, T. K.; Stults, M.; Suleiman, Y. Y.; Van Fossen, M.; Weertman, B.

2015-12-01

The IRIS Data Management Center (DMC) has served the seismological community for nearly 25 years. In that time we have offered data and information from our archive using a variety of mechanisms ranging from email-based to desktop applications to web applications and web services. Of these, web services have quickly become the primary method for data extraction at the DMC. In 2011, the first full year of operation, web services accounted for over 40% of the data shipped from the DMC. In 2014, over ~450 TB of data was delivered directly to users through web services, representing nearly 70% of all shipments from the DMC that year. In addition to handling requests directly from users, the DMC switched all data extraction methods to use web services in 2014. On average the DMC now handles between 10 and 20 million requests per day submitted to web service interfaces. The rapid adoption of web services is attributed to the many advantages they bring. For users, they provide on-demand data using an interface technology, HTTP, that is widely supported in nearly every computing environment and language. These characteristics, combined with human-readable documentation and existing tools make integration of data access into existing workflows relatively easy. For the DMC, the web services provide an abstraction layer to internal repositories allowing for concentrated optimization of extraction workflow and easier evolution of those repositories. Lending further support to DMC's push in this direction, the core web services for station metadata, timeseries data and event parameters were adopted as standards by the International Federation of Digital Seismograph Networks (FDSN). We expect to continue enhancing existing services and building new capabilities for this platform. For example, the DMC has created a federation system and tools allowing researchers to discover and collect seismic data from data centers running the FDSN-standardized services. A future capability will leverage the DMC's MUSTANG project to select data based on data quality measurements. Within five years, the DMC's web services have proven to be a robust and flexible platform that enables continued growth for the DMC. We expect continued enhancements and adoption of web services.

NGL Viewer: a web application for molecular visualization

PubMed Central

Rose, Alexander S.; Hildebrand, Peter W.

2015-01-01

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

The ADAM project: a generic web interface for retrieval and display of ATLAS TDAQ information

NASA Astrophysics Data System (ADS)

Harwood, A.; Lehmann Miotto, G.; Magnoni, L.; Vandelli, W.; Savu, D.

2012-06-01

This paper describes a new approach to the visualization of information about the operation of the ATLAS Trigger and Data Acquisition system. ATLAS is one of the two general purpose detectors positioned along the Large Hadron Collider at CERN. Its data acquisition system consists of several thousand computers interconnected via multiple gigabit Ethernet networks, that are constantly monitored via different tools. Operational parameters ranging from the temperature of the computers to the network utilization are stored in several databases for later analysis. Although the ability to view these data-sets individually is already in place, currently there is no way to view this data together, in a uniform format, from one location. The ADAM project has been launched in order to overcome this limitation. It defines a uniform web interface to collect data from multiple providers that have different structures. It is capable of aggregating and correlating the data according to user defined criteria. Finally, it visualizes the collected data using a flexible and interactive front-end web system. Structurally, the project comprises of 3 main levels of the data collection cycle: The Level 0 represents the information sources within ATLAS. These providers do not store information in a uniform fashion. The first step of the project was to define a common interface with which to expose stored data. The interface designed for the project originates from the Google Data Protocol API. The idea is to allow read-only access to data providers, through HTTP requests similar in format to the SQL query structure. This provides a standardized way to access this different information sources within ATLAS. The Level 1 can be considered the engine of the system. The primary task of the Level 1 is to gather data from multiple data sources via the common interface, to correlate this data together, or over a defined time series, and expose the combined data as a whole to the Level 2 web interface. The Level 2 is designed to present the data in a similar style and aesthetic, despite the different data sources. Pages can be constructed, edited and personalized by users to suit the specific data being shown. Pages can show a collection of graphs displaying data potentially coming from multiple sources. The project as a whole has a great amount of scope thanks to the uniform approach chosen for exposing data, and the flexibility of the Level 2 in presenting results. The paper will describe in detail the design and implementation of this new tool. In particular we will go through the project architecture, the implementation choices and the examples of usage of the system in place within the ATLAS TDAQ infrastructure.

The GLOBE Visualization Project: Using WWW in the Classroom.

ERIC Educational Resources Information Center

de La Beaujardiere, J-F; And Others

1997-01-01

Describes a World Wide Web-based, user-friendly, language-independent graphical user interface providing access to visualizations created for GLOBE (Global Learning and Observations to Benefit the Environment), a multinational program of education and science. (DDR)

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

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

Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

2002-01-01

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easymore » access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.« less

Dynamic User Interfaces for Service Oriented Architectures in Healthcare.

PubMed

Schweitzer, Marco; Hoerbst, Alexander

2016-01-01

Electronic Health Records (EHRs) play a crucial role in healthcare today. Considering a data-centric view, EHRs are very advanced as they provide and share healthcare data in a cross-institutional and patient-centered way adhering to high syntactic and semantic interoperability. However, the EHR functionalities available for the end users are rare and hence often limited to basic document query functions. Future EHR use necessitates the ability to let the users define their needed data according to a certain situation and how this data should be processed. Workflow and semantic modelling approaches as well as Web services provide means to fulfil such a goal. This thesis develops concepts for dynamic interfaces between EHR end users and a service oriented eHealth infrastructure, which allow the users to design their flexible EHR needs, modeled in a dynamic and formal way. These are used to discover, compose and execute the right Semantic Web services.

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

FASTQ quality control dashboard

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

2016-07-25

FQCDB builds up existing open source software, FastQC, implementing a modern web interface for across parsed output of FastQC. In addition, FQCDB is extensible as a web service to include additional plots of type line, boxplot, or heatmap, across data formatted according to guidelines. The interface is also configurable via more readable JSON format, enabling customization by non-web programmers.

Web mapping system for complex processing and visualization of environmental geospatial datasets

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny; Okladnikov, Igor

2016-04-01

Environmental geospatial datasets (meteorological observations, modeling and reanalysis results, etc.) are used in numerous research applications. Due to a number of objective reasons such as inherent heterogeneity of environmental datasets, big dataset volume, complexity of data models used, syntactic and semantic differences that complicate creation and use of unified terminology, the development of environmental geodata access, processing and visualization services as well as client applications turns out to be quite a sophisticated task. According to general INSPIRE requirements to data visualization geoportal web applications have to provide such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. It should be noted that modern web mapping systems as integrated geoportal applications are developed based on the SOA and might be considered as complexes of interconnected software tools for working with geospatial data. In the report a complex web mapping system including GIS web client and corresponding OGC services for working with geospatial (NetCDF, PostGIS) dataset archive is presented. There are three basic tiers of the GIS web client in it: 1. Tier of geospatial metadata retrieved from central MySQL repository and represented in JSON format 2. Tier of JavaScript objects implementing methods handling: --- NetCDF metadata --- Task XML object for configuring user calculations, input and output formats --- OGC WMS/WFS cartographical services 3. Graphical user interface (GUI) tier representing JavaScript objects realizing web application business logic Metadata tier consists of a number of JSON objects containing technical information describing geospatial datasets (such as spatio-temporal resolution, meteorological parameters, valid processing methods, etc). The middleware tier of JavaScript objects implementing methods for handling geospatial metadata, task XML object, and WMS/WFS cartographical services interconnects metadata and GUI tiers. The methods include such procedures as JSON metadata downloading and update, launching and tracking of the calculation task running on the remote servers as well as working with WMS/WFS cartographical services including: obtaining the list of available layers, visualizing layers on the map, exporting layers in graphical (PNG, JPG, GeoTIFF), vector (KML, GML, Shape) and digital (NetCDF) formats. Graphical user interface tier is based on the bundle of JavaScript libraries (OpenLayers, GeoExt and ExtJS) and represents a set of software components implementing web mapping application business logic (complex menus, toolbars, wizards, event handlers, etc.). GUI provides two basic capabilities for the end user: configuring the task XML object functionality and cartographical information visualizing. The web interface developed is similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Web mapping system developed has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical form. The work is supported by SB RAS Basic Program Projects VIII.80.2.1 and IV.38.1.7.

A Web Based Approach to Integrate Space Culture and Education

NASA Astrophysics Data System (ADS)

Gerla, F.

2002-01-01

Our intention is to dedicate a large section of our web site to space education. As the national User Support and Operation Center (USOC) for the International Space Station, MARS Center is also willing to provide material, such as videos and data, for educational purposes. In order to base our initiative on authoritative precedents, our first step has been a comparative analysis between different space agency education web sites, such as ESA and NASA. As is well known, Internet is a powerful reality, capable of connecting people all over the world and rendering public a huge amount of information. The first problem, then, is to organize this information, in order to use the web as an efficient education tool. That is why studies such as User Modeling (UM), Human Computer Interaction (HCI) and Semantic Web have become more important in Information Technology and Science. Traditional search engines are unable to provide an optimal retrieval of contents really searched for by users. Semantic Web is a valid alternative: according to its theories, web information should be represented using metadata language. Users should be able and enabled to successfully search, obtain and study new information from web. Forging knowledge in an intelligent manner, preventing users from making errors, and making this formidable quantity of information easily available have also been the starting points for HCI methodologies for defining Adaptable Interfaces. Here the information is divided into different sets, on the basis of the intended user profile, in order to prevent users from getting lost. Realized as an adaptable interface, an education web site can help users to effectively retrieve the information necessary for their scopes (teaching for a teacher and learning for a student). For students it's a great advantage to use interfaces designed on the basis of their age and scholastic level. Indeed, an adaptable interface is intended not just for students, but also for teachers, who can use it to prepare their lessons, retrieve information and organize the didactic material in order to support their lessons. We think it important to use a user centered "psychology" based on UM: we have to know the needs and expectations of the students. Our intent is to use usability tests not just to prove the site effectiveness and clearness, but also to investigate aesthetical preferences of children and young people. Physics, mathematics, chemistry are just some of the difficult learning fields connected with space technologies. Space culture is a potentially never-ending field, and our scope will be to lead students by hand in this universe of knowledge. This paper will present MARS activities in the framework of the above methodologies aimed at implementing a web based approach to integrate space culture and education. The activities are already in progress and some results will be presented in the final paper.

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

PubMed

Jung, Tae-Sung; Yeo, Hock Chuan; Reddy, Satty G; Cho, Wan-Sup; Lee, Dong-Yup

2009-11-01

WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions. WEbcoli is freely accessible at http://webcoli.org. cheld@nus.edu.sg.

Interoperability And Value Added To Earth Observation Data

NASA Astrophysics Data System (ADS)

Gasperi, J.

2012-04-01

Geospatial web services technology has provided a new means for geospatial data interoperability. Open Geospatial Consortium (OGC) services such as Web Map Service (WMS) to request maps on the Internet, Web Feature Service (WFS) to exchange vectors or Catalog Service for the Web (CSW) to search for geospatialized data have been widely adopted in the Geosciences community in general and in the remote sensing community in particular. These services make Earth Observation data available to a wider range of public users than ever before. The mapshup web client offers an innovative and efficient user interface that takes advantage of the power of interoperability. This presentation will demonstrate how mapshup can be effectively used in the context of natural disasters management.

FwWebViewPlus: integration of web technologies into WinCC OA based Human-Machine Interfaces at CERN

NASA Astrophysics Data System (ADS)

Golonka, Piotr; Fabian, Wojciech; Gonzalez-Berges, Manuel; Jasiun, Piotr; Varela-Rodriguez, Fernando

2014-06-01

The rapid growth in popularity of web applications gives rise to a plethora of reusable graphical components, such as Google Chart Tools and JQuery Sparklines, implemented in JavaScript and run inside a web browser. In the paper we describe the tool that allows for seamless integration of web-based widgets into WinCC Open Architecture, the SCADA system used commonly at CERN to build complex Human-Machine Interfaces. Reuse of widely available widget libraries and pushing the development efforts to a higher abstraction layer based on a scripting language allow for significant reduction in maintenance of the code in multi-platform environments compared to those currently used in C++ visualization plugins. Adequately designed interfaces allow for rapid integration of new web widgets into WinCC OA. At the same time, the mechanisms familiar to HMI developers are preserved, making the use of new widgets "native". Perspectives for further integration between the realms of WinCC OA and Web development are also discussed.

THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

The new THttpServer class in ROOT implements HTTP server for arbitrary ROOT applications. It is based on Civetweb embeddable HTTP server and provides direct access to all objects registered for the server. Objects data could be provided in different formats: binary, XML, GIF/PNG, and JSON. A generic user interface for THttpServer has been implemented with HTML/JavaScript based on JavaScript ROOT development. With any modern web browser one could list, display, and monitor objects available on the server. THttpServer is used in Go4 framework to provide HTTP interface to the online analysis.

Amino Acid Interaction (INTAA) web server.

PubMed

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

PubMed

Correa, Miria C; Deus, Helena F; Vasconcelos, Ana T; Hayashi, Yuki; Ajani, Jaffer A; Patnana, Srikrishna V; Almeida, Jonas S

2010-10-26

AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine.

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

PubMed

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

2006-06-30

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

WebLogo: A Sequence Logo Generator

PubMed Central

Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc; Brenner, Steven E.

2004-01-01

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization. PMID:15173120

A RESTful API for accessing microbial community data for MG-RAST.

PubMed

Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M; Desai, Narayan; Meyer, Folker

2015-01-01

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.

Modelling Safe Interface Interactions in Web Applications

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Cabot, Jordi; Grossniklaus, Michael

Current Web applications embed sophisticated user interfaces and business logic. The original interaction paradigm of the Web based on static content pages that are browsed by hyperlinks is, therefore, not valid anymore. In this paper, we advocate a paradigm shift for browsers and Web applications, that improves the management of user interaction and browsing history. Pages are replaced by States as basic navigation nodes, and Back/Forward navigation along the browsing history is replaced by a full-fledged interactive application paradigm, supporting transactions at the interface level and featuring Undo/Redo capabilities. This new paradigm offers a safer and more precise interaction model, protecting the user from unexpected behaviours of the applications and the browser.

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."

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

iDrug: a web-accessible and interactive drug discovery and design platform

PubMed Central

2014-01-01

Background The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. As programs are developed by various research groups, a consistent user-friendly online graphical working environment, combining computational techniques such as pharmacophore mapping, similarity calculation, scoring, and target identification is needed. Results We presented a versatile, user-friendly, and efficient online tool for computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing. All the customized configurations of the functional modules can be accessed through featured session files provided, which can be saved to the local disk and uploaded to resume or update the history work. Conclusions iDrug is easy to use, and provides a novel, fast and reliable tool for conducting drug design experiments. By using iDrug, various molecular design processing tasks can be submitted and visualized simply in one browser without installing locally any standalone modeling softwares. iDrug is accessible free of charge at http://lilab.ecust.edu.cn/idrug. PMID:24955134

Integrating hydrologic modeling web services with online data sharing to prepare, store, and execute models in hydrology

NASA Astrophysics Data System (ADS)

Gan, T.; Tarboton, D. G.; Dash, P. K.; Gichamo, T.; Horsburgh, J. S.

2017-12-01

Web based apps, web services and online data and model sharing technology are becoming increasingly available to support research. This promises benefits in terms of collaboration, platform independence, transparency and reproducibility of modeling workflows and results. However, challenges still exist in real application of these capabilities and the programming skills researchers need to use them. In this research we combined hydrologic modeling web services with an online data and model sharing system to develop functionality to support reproducible hydrologic modeling work. We used HydroDS, a system that provides web services for input data preparation and execution of a snowmelt model, and HydroShare, a hydrologic information system that supports the sharing of hydrologic data, model and analysis tools. To make the web services easy to use, we developed a HydroShare app (based on the Tethys platform) to serve as a browser based user interface for HydroDS. In this integration, HydroDS receives web requests from the HydroShare app to process the data and execute the model. HydroShare supports storage and sharing of the results generated by HydroDS web services. The snowmelt modeling example served as a use case to test and evaluate this approach. We show that, after the integration, users can prepare model inputs or execute the model through the web user interface of the HydroShare app without writing program code. The model input/output files and metadata describing the model instance are stored and shared in HydroShare. These files include a Python script that is automatically generated by the HydroShare app to document and reproduce the model input preparation workflow. Once stored in HydroShare, inputs and results can be shared with other users, or published so that other users can directly discover, repeat or modify the modeling work. This approach provides a collaborative environment that integrates hydrologic web services with a data and model sharing system to enable model development and execution. The entire system comprised of the HydroShare app, HydroShare and HydroDS web services is open source and contributes to capability for web based modeling research.

TMFoldWeb: a web server for predicting transmembrane protein fold class.

PubMed

Kozma, Dániel; Tusnády, Gábor E

2015-09-17

Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices.

Implementation of a scalable, web-based, automated clinical decision support risk-prediction tool for chronic kidney disease using C-CDA and application programming interfaces.

PubMed

Samal, Lipika; D'Amore, John D; Bates, David W; Wright, Adam

2017-11-01

Clinical decision support tools for risk prediction are readily available, but typically require workflow interruptions and manual data entry so are rarely used. Due to new data interoperability standards for electronic health records (EHRs), other options are available. As a clinical case study, we sought to build a scalable, web-based system that would automate calculation of kidney failure risk and display clinical decision support to users in primary care practices. We developed a single-page application, web server, database, and application programming interface to calculate and display kidney failure risk. Data were extracted from the EHR using the Consolidated Clinical Document Architecture interoperability standard for Continuity of Care Documents (CCDs). EHR users were presented with a noninterruptive alert on the patient's summary screen and a hyperlink to details and recommendations provided through a web application. Clinic schedules and CCDs were retrieved using existing application programming interfaces to the EHR, and we provided a clinical decision support hyperlink to the EHR as a service. We debugged a series of terminology and technical issues. The application was validated with data from 255 patients and subsequently deployed to 10 primary care clinics where, over the course of 1 year, 569 533 CCD documents were processed. We validated the use of interoperable documents and open-source components to develop a low-cost tool for automated clinical decision support. Since Consolidated Clinical Document Architecture-based data extraction extends to any certified EHR, this demonstrates a successful modular approach to clinical decision support. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

Cybersecurity has become a great concern as threats of service interruption, unauthorized access, stealing and altering of information, and spreading of viruses have become more prevalent and serious. Application layer access control of applications is a critical component in the overall security solution that also includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. An access control solution, based on an open-source access manager augmented with custom software components, was developed to provide protection to both Web-based and Javabased client and server applications. The DISA Security Service (DISA-SS) provides common access control capabilities for AMMOS software applications through a set of application programming interfaces (APIs) and network- accessible security services for authentication, single sign-on, authorization checking, and authorization policy management. The OpenAM access management technology designed for Web applications can be extended to meet the needs of Java thick clients and stand alone servers that are commonly used in the JPL AMMOS environment. The DISA-SS reusable components have greatly reduced the effort for each AMMOS subsystem to develop its own access control strategy. The novelty of this work is that it leverages an open-source access management product that was designed for Webbased applications to provide access control for Java thick clients and Java standalone servers. Thick clients and standalone servers are still commonly used in businesses and government, especially for applications that require rich graphical user interfaces and high-performance visualization that cannot be met by thin clients running on Web browsers

Architecture, Design, and Development of an HTML/JavaScript Web-Based Group Support System.

ERIC Educational Resources Information Center

Romano, Nicholas C., Jr.; Nunamaker, Jay F., Jr.; Briggs, Robert O.; Vogel, Douglas R.

1998-01-01

Examines the need for virtual workspaces and describes the architecture, design, and development of GroupSystems for the World Wide Web (GSWeb), an HTML/JavaScript Web-based Group Support System (GSS). GSWeb, an application interface similar to a Graphical User Interface (GUI), is currently used by teams around the world and relies on user…

Oyster Fisheries App

NASA Technical Reports Server (NTRS)

Perez Guerrero, Geraldo A.; Armstrong, Duane; Underwood, Lauren

2015-01-01

This project is creating a cloud-enabled, HTML 5 web application to help oyster fishermen and state agencies apply Earth science to improve the management of this important natural and economic resource. The Oyster Fisheries app gathers and analyzes environmental and water quality information, and alerts fishermen and resources managers about problems in oyster fishing waters. An intuitive interface based on Google Maps displays the geospatial information and provides familiar interactive controls to the users. Alerts can be tailored to notify users when conditions in specific leases or public fishing areas require attention. The app is hosted on the Amazon Web Services cloud. It is being developed and tested using some of the latest web development tools such as web components and Polymer.

"WWW.MDTF.ORG": a World Wide Web forum for developing open-architecture, freely distributed, digital teaching file software by participant consensus.

PubMed

Katzman, G L; Morris, D; Lauman, J; Cochella, C; Goede, P; Harnsberger, H R

2001-06-01

To foster a community supported evaluation processes for open-source digital teaching file (DTF) development and maintenance. The mechanisms used to support this process will include standard web browsers, web servers, forum software, and custom additions to the forum software to potentially enable a mediated voting protocol. The web server will also serve as a focal point for beta and release software distribution, which is the desired end-goal of this process. We foresee that www.mdtf.org will provide for widespread distribution of open source DTF software that will include function and interface design decisions from community participation on the website forums.

Final Report for DOE Project: Portal Web Services: Support of DOE SciDAC Collaboratories

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

Mary Thomas, PI; Geoffrey Fox, Co-PI; Gannon, D

2007-10-01

Grid portals provide the scientific community with familiar and simplified interfaces to the Grid and Grid services, and it is important to deploy grid portals onto the SciDAC grids and collaboratories. The goal of this project is the research, development and deployment of interoperable portal and web services that can be used on SciDAC National Collaboratory grids. This project has four primary task areas: development of portal systems; management of data collections; DOE science application integration; and development of web and grid services in support of the above activities.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

ChRIS--A web-based neuroimaging and informatics system for collecting, organizing, processing, visualizing and sharing of medical data.

PubMed

Pienaar, Rudolph; Rannou, Nicolas; Bernal, Jorge; Hahn, Daniel; Grant, P Ellen

2015-01-01

The utility of web browsers for general purpose computing, long anticipated, is only now coming into fruition. In this paper we present a web-based medical image data and information management software platform called ChRIS ([Boston] Children's Research Integration System). ChRIS' deep functionality allows for easy retrieval of medical image data from resources typically found in hospitals, organizes and presents information in a modern feed-like interface, provides access to a growing library of plugins that process these data - typically on a connected High Performance Compute Cluster, allows for easy data sharing between users and instances of ChRIS and provides powerful 3D visualization and real time collaboration.

The Virtual Solar-Terrestrial Observatory; access to and use of diverse solar and solar- terrestrial data.

NASA Astrophysics Data System (ADS)

Fox, P.; McGuinness, D.; Cinquini, L.; West, P.; Garcia, J.; Zednik, S.; Benedict, J.

2008-05-01

This presentation will demonstrate how users and other data providers can utilize the Virtual Solar-Terrestrial Observatory (VSTO) to find, access and use diverse data holdings from the disciplines of solar, solar-terrestrial and space physics. VSTO provides a web portal, web services and a native applications programming interface for various levels of users. Since these access methods are based on semantic web technologies and refer to the VSTO ontology, users also have the option of taking advantage of value added services when accessing and using the data. We present example of both conventional use of VSTO as well as the advanced semantics use. Finally, we present our future directions for VSTO and semantic data frameworks in general.

The Virtual Solar-Terrestrial Observatory; access to and use of diverse solar and solar-terrestrial data

NASA Astrophysics Data System (ADS)

Fox, P.

2007-05-01

This presentation will demonstrate how users and other data providers can utilize the Virtual Solar-Terrestrial Observatory (VSTO) to find, access and use diverse data holdings from the disciplines of solar, solar-terrestrial and space physics. VSTO provides a web portal, web services and a native applications programming interface for various levels of users. Since these access methods are based on semantic web technologies and refer to the VSTO ontology, users also have the option of taking advantage of value added services when accessing and using the data. We present example of both conventional use of VSTO as well as the advanced semantics use. Finally, we present our future directions for VSTO and semantic data frameworks in general.

Usability testing of existing type 2 diabetes mellitus websites.

PubMed

Davis, Dorian; Jiang, Steven

2016-08-01

Given the significant increase in the use of the internet as an educational tool for diabetes, very little research has been published on the usability of healthcare websites, even though it is a determining factor for user satisfaction. The aim of this study is to evaluate and critique the interfaces of existing diabetes websites for usability concerns and provide design solutions for improvement. Emphasis is placed on Type 2 Diabetes Mellitus since it is the most common and life threatening form of diabetes. A usability test was performed on the interfaces of three existing diabetes websites, American Diabetes Association (www.diabetes.org), WebMD (www.webmd.com) and the National Diabetes Education Program (ndep.nih.gov). The goal was to collect qualitative and quantitative data to determine: (1) if participants are able to complete specified tasks successfully; (2) the length of time it takes participants to complete the specified tasks and; (3) participants' satisfaction with the three websites. Twenty adults, 18 years of age and older participated in the study. The results from the MANOVA test revealed a significant difference between the three websites for number of clicks, number of errors and completion time when analyzed simultaneously. The ANOVA tests revealed a significant difference for all three variables. The Student-Newman-Keuls (SNK) test shows a significant difference for completion time between American Diabetes Association and WebMD. A significant difference was found for the number of clicks for the National Diabetes Education Program compared to the American Diabetes Association and WebMD. However, no significant difference was found for the number of clicks between American Diabetes Association and WebMD. Lastly, a significant difference was found between each interface for number of errors. Although, the American Diabetes Association web-interface was most favorable, there were many positive design elements for each interface. On the other hand, the significant amount of information overload experienced for each website left participants feeling perplexed. Thus, innovative solutions are needed to reduce information overload and ensure users are engaged and empowered to make informed decisions about their healthcare. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Addressing data access challenges in seismology

NASA Astrophysics Data System (ADS)

Trabant, C. M.; Ahern, T.; Weertman, B.; Benson, R. B.; Van Fossen, M.; Weekly, R. T.; Casey, R. E.; Suleiman, Y. Y.; Stults, M.

2016-12-01

The development of web services at the IRIS Data Management Center (DMC) over the last 6 years represents the most significant enhancement of data access ever introduced at the DMC. These web services have allowed the us to focus our internal operations around a single, consistent data access layer while facilitating development of a new generation of tools and methods for researchers to conduct their work. This effort led the DMC to propose standardized web service interfaces within the International Federation of Digital Seismograph Networks (FDSN), enabling other seismological data centers to offer data using compatible interfaces. With this new foundation, we now turn our attention to more advanced data access challenges. In particular, we will present the status of two developments intending to address 1) access to data of consistent quality for science and 2) discovery and access of data from multiple data centers. To address the challenge of requesting high or consistent quality data we will introduce our Research-Ready Data Sets (RRDS) initiative. The purpose of the RRDS project is to reduce the time a researcher spends culling and otherwise identifying data appropriate for given study. RRDS will provide users with additional criteria related to data quality that can be specified when requesting data. Leveraging the data quality measurements provided by our MUSTANG system, these criteria will include ambient noise, completeness, dead channel identification and more. To address the challenge of seismological data discovery and access, we have built and continue to improve the IRIS Federator. The Federator takes advantage of the FDSN-standard web services at various data centers to help a user locate specific channels, wherever they may be offered globally. The search interface provides results that are pre-formatted requests, ready for submission to each data center that serves that data. These two developments are aimed squarely at reducing the time researchers spend searching for, collecting and preparing data for processing.

A Randomized Trial Comparing Classical Participatory Design to VandAID, an Interactive CrowdSourcing Platform to Facilitate User-centered Design.

PubMed

Dufendach, Kevin R; Koch, Sabine; Unertl, Kim M; Lehmann, Christoph U

2017-10-26

Early involvement of stakeholders in the design of medical software is particularly important due to the need to incorporate complex knowledge and actions associated with clinical work. Standard user-centered design methods include focus groups and participatory design sessions with individual stakeholders, which generally limit user involvement to a small number of individuals due to the significant time investments from designers and end users. The goal of this project was to reduce the effort for end users to participate in co-design of a software user interface by developing an interactive web-based crowdsourcing platform. In a randomized trial, we compared a new web-based crowdsourcing platform to standard participatory design sessions. We developed an interactive, modular platform that allows responsive remote customization and design feedback on a visual user interface based on user preferences. The responsive canvas is a dynamic HTML template that responds in real time to user preference selections. Upon completion, the design team can view the user's interface creations through an administrator portal and download the structured selections through a REDCap interface. We have created a software platform that allows users to customize a user interface and see the results of that customization in real time, receiving immediate feedback on the impact of their design choices. Neonatal clinicians used the new platform to successfully design and customize a neonatal handoff tool. They received no specific instruction and yet were able to use the software easily and reported high usability. VandAID, a new web-based crowdsourcing platform, can involve multiple users in user-centered design simultaneously and provides means of obtaining design feedback remotely. The software can provide design feedback at any stage in the design process, but it will be of greatest utility for specifying user requirements and evaluating iterative designs with multiple options.

Automatic and continuous landslide monitoring: the Rotolon Web-based platform

NASA Astrophysics Data System (ADS)

Frigerio, Simone; Schenato, Luca; Mantovani, Matteo; Bossi, Giulia; Marcato, Gianluca; Cavalli, Marco; Pasuto, Alessandro

2013-04-01

Mount Rotolon (Eastern Italian Alps) is affected by a complex landslide that, since 1985, is threatening the nearby village of Recoaro Terme. The first written proof of a landslide occurrence dated back to 1798. After the last re-activation on November 2010 (637 mm of intense rainfall recorded in the 12 days prior the event), a mass of approximately 320.000 m3 detached from the south flank of Mount Rotolon and evolved into a fast debris flow that ran for about 3 km along the stream bed. A real-time monitoring system was required to detect early indication of rapid movements, potentially saving lives and property. A web-based platform for automatic and continuous monitoring was designed as a first step in the implementation of an early-warning system. Measurements collected by the automated geotechnical and topographic instrumentation, deployed over the landslide body, are gathered in a central box station. After the calibration process, they are transmitted by web services on a local server, where graphs, maps, reports and alert announcement are automatically generated and updated. All the processed information are available by web browser with different access rights. The web environment provides the following advantages: 1) data is collected from different data sources and matched on a single server-side frame 2) a remote user-interface allows regular technical maintenance and direct access to the instruments 3) data management system is synchronized and automatically tested 4) a graphical user interface on browser provides a user-friendly tool for decision-makers to interact with a system continuously updated. On this site two monitoring systems are actually on course: 1) GB-InSAR radar interferometer (University of Florence - Department of Earth Science) and 2) Automated Total Station (ATS) combined with extensometers network in a Web-based solution (CNR-IRPI Padova). This work deals with details on methodology, services and techniques adopted for the second monitoring solution. The activity directly interfaces with local Civil Protection agency, Regional Geological Service and local authorities with integrated roles and aims.

DyNAVacS: an integrative tool for optimized DNA vaccine design.

PubMed

Harish, Nagarajan; Gupta, Rekha; Agarwal, Parul; Scaria, Vinod; Pillai, Beena

2006-07-01

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL: http://miracle.igib.res.in/dynavac/.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Micklem, Gos; Kawashima, Shuichi; Yamaguchi, Atsuko; Nakao, Mitsuteru; Yamamoto, Yasunori; Okamoto, Shinobu; Oouchida, Kenta; Chun, Hong-Woo; Aerts, Jan; Afzal, Hammad; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Belleau, Francois; Bolleman, Jerven; Bonnal, Raoul Jp; Chapman, Brad; Cock, Peter Ja; Eriksson, Tore; Gordon, Paul Mk; Goto, Naohisa; Hayashi, Kazuhiro; Horn, Heiko; Ishiwata, Ryosuke; Kaminuma, Eli; Kasprzyk, Arek; Kawaji, Hideya; Kido, Nobuhiro; Kim, Young Joo; Kinjo, Akira R; Konishi, Fumikazu; Kwon, Kyung-Hoon; Labarga, Alberto; Lamprecht, Anna-Lena; Lin, Yu; Lindenbaum, Pierre; McCarthy, Luke; Morita, Hideyuki; Murakami, Katsuhiko; Nagao, Koji; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Prins, Pjotr; Saito, Taro L; Samwald, Matthias; Satagopam, Venkata P; Shigemoto, Yasumasa; Smith, Richard; Splendiani, Andrea; Sugawara, Hideaki; Taylor, James; Vos, Rutger A; Withers, David; Yamasaki, Chisato; Zmasek, Christian M; Kawamoto, Shoko; Okubo, Kosaku; Asai, Kiyoshi; Takagi, Toshihisa

2013-02-11

BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

PubMed Central

2013-01-01

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. PMID:23398680

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

PubMed Central

2010-01-01

Background Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. Results In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. Conclusions CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu. PMID:20946609

Advancements in Data Access at the IRIS Data Management Center to Broaden Data Use

NASA Astrophysics Data System (ADS)

Benson, R. B.; Trabant, C. M.; Ahern, T. K.

2013-12-01

The IRIS Data Management Center (DMC) has been serving digital seismic data for more than 20 years and has offered a variety of access mechanisms that have stood the test of time. However, beginning in 2010, and in response to multiple needs being requested from the IRIS DMC, we have developed web service interfaces to access our primary data repository. These new interfaces have rapidly grown in popularity. In 2013, the third full year of their operation, these services were responsible for half of all the data shipped from the DMC. In the same time period, the amount of data shipped from the other data access mechanisms has also increased. This non-linear growth of data shipments reflects the increased data usage by the research community. We believe that our new web service interfaces are well suited to fit future data access needs and signify a significant evolution in integrating different scientific data sets. Based on standardized web technologies, support for writing access software is ubiquitous. As fundamentally programmatic interfaces, the services are well suited for integration into data processing systems, in particular large-scale data processing systems. Their programmatic nature also makes then well suited for use with brokering systems where, for example, data from multiple disciplines can be integrated. In addition to providing access to raw data, the DMC created web services that apply simple, on-the-fly processing and format conversion. Processing the data (e.g. converting to Earth units) and formatting the result into something generally usable (e.g. ASCII) removes important barriers for users working in other disciplines. The end result is that we are shipping a much larger amount of data in a manner more directly usable by users. Many of these principles will be applied to the DMC's future work in the NSF's EarthCube Web Service Building Blocks project.

Change and Anomaly Detection in Real-Time GPS Data

NASA Astrophysics Data System (ADS)

Granat, R.; Pierce, M.; Gao, X.; Bock, Y.

2008-12-01

The California Real-Time Network (CRTN) is currently generating real-time GPS position data at a rate of 1-2Hz at over 80 locations. The CRTN data presents the possibility of studying dynamical solid earth processes in a way that complements existing seismic networks. To realize this possibility we have developed a prototype system for detecting changes and anomalies in the real-time data. Through this system, we can can correlate changes in multiple stations in order to detect signals with geographical extent. Our approach involves developing a statistical model for each GPS station in the network, and then using those models to segment the time series into a number of discrete states described by the model. We use a hidden Markov model (HMM) to describe the behavior of each station; fitting the model to the data requires neither labeled training examples nor a priori information about the system. As such, HMMs are well suited to this problem domain, in which the data remains largely uncharacterized. There are two main components to our approach. The first is the model fitting algorithm, regularized deterministic annealing expectation- maximization (RDAEM), which provides robust, high-quality results. The second is a web service infrastructure that connects the data to the statistical modeling analysis and allows us to easily present the results of that analysis through a web portal interface. This web service approach facilitates the automatic updating of station models to keep pace with dynamical changes in the data. Our web portal interface is critical to the process of interpreting the data. A Google Maps interface allows users to visually interpret state changes not only on individual stations but across the entire network. Users can drill down from the map interface to inspect detailed results for individual stations, download the time series data, and inspect fitted models. Alternatively, users can use the web portal look at the evolution of changes on the network by moving backwards and forwards in time.

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

PubMed

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu.

How do I order MISR data?

Atmospheric Science Data Center

2017-10-12

... and archived at the NASA Langley Research Center Atmospheric Science Data Center (ASDC). A MISR Order and Customization Tool is ... Pool (an on-line, short-term data cache that provides a Web interface and FTP access). Specially subsetted and/or reformatted MISR data ...

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

PubMed Central

Abdulrehman, Dário; Monteiro, Pedro Tiago; Teixeira, Miguel Cacho; Mira, Nuno Pereira; Lourenço, Artur Bastos; dos Santos, Sandra Costa; Cabrito, Tânia Rodrigues; Francisco, Alexandre Paulo; Madeira, Sara Cordeiro; Aires, Ricardo Santos; Oliveira, Arlindo Limede; Sá-Correia, Isabel; Freitas, Ana Teresa

2011-01-01

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) information system (http://www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2010, this database contains over 48 200 regulatory associations between transcription factors (TFs) and target genes, including 298 specific DNA-binding sites for 110 characterized TFs. All regulatory associations stored in the database were revisited and detailed information on the experimental evidences that sustain those associations was added and classified as direct or indirect evidences. The inclusion of this new data, gathered in response to the requests of YEASTRACT users, allows the user to restrict its queries to subsets of the data based on the existence or not of experimental evidences for the direct action of the TFs in the promoter region of their target genes. Another new feature of this release is the availability of all data through a machine readable web-service interface. Users are no longer restricted to the set of available queries made available through the existing web interface, and can use the web service interface to query, retrieve and exploit the YEASTRACT data using their own implementation of additional functionalities. The YEASTRACT information system is further complemented with several computational tools that facilitate the use of the curated data when answering a number of important biological questions. Since its first release in 2006, YEASTRACT has been extensively used by hundreds of researchers from all over the world. We expect that by making the new data and services available, the system will continue to be instrumental for yeast biologists and systems biology researchers. PMID:20972212

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

Quarterly Performance/Technical Report of the National Marrow Donor Program

DTIC Science & Technology

2006-05-01

HapLogicTM was implemented for all search reports. This provides a real-time DNA - based match that utilizes genotype list data in the up- front match...CCN meeting held at the ASBMT/CIBMTR Tandem conference, the National Library of Medicine (NLM) demonstrated a draft of their web based version of the...making improvements to the web based interface. O Government Signature Date A . Contingency Preparedness (Hypothesis 1) Grant Award N00014-05-1-0859

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.

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

PubMed

Ramirez-Gonzalez, Ricardo; Caccamo, Mario; MacLean, Daniel

2011-10-01

Scientists now use high-throughput sequencing technologies and short-read assembly methods to create draft genome assemblies in just days. Tools and pipelines like the assembler, and the workflow management environments make it easy for a non-specialist to implement complicated pipelines to produce genome assemblies and annotations very quickly. Such accessibility results in a proliferation of assemblies and associated files, often for many organisms. These assemblies get used as a working reference by lots of different workers, from a bioinformatician doing gene prediction or a bench scientist designing primers for PCR. Here we describe Gee Fu, a database tool for genomic assembly and feature data, including next-generation sequence alignments. Gee Fu is an instance of a Ruby-On-Rails web application on a feature database that provides web and console interfaces for input, visualization of feature data via AnnoJ, access to data through a web-service interface, an API for direct data access by Ruby scripts and access to feature data stored in BAM files. Gee Fu provides a platform for storing and sharing different versions of an assembly and associated features that can be accessed and updated by bench biologists and bioinformaticians in ways that are easy and useful for each. http://tinyurl.com/geefu dan.maclean@tsl.ac.uk.

Data Access System for Hydrology

NASA Astrophysics Data System (ADS)

Whitenack, T.; Zaslavsky, I.; Valentine, D.; Djokic, D.

2007-12-01

As part of the CUAHSI HIS (Consortium of Universities for the Advancement of Hydrologic Science, Inc., Hydrologic Information System), the CUAHSI HIS team has developed Data Access System for Hydrology or DASH. DASH is based on commercial off the shelf technology, which has been developed in conjunction with a commercial partner, ESRI. DASH is a web-based user interface, developed in ASP.NET developed using ESRI ArcGIS Server 9.2 that represents a mapping, querying and data retrieval interface over observation and GIS databases, and web services. This is the front end application for the CUAHSI Hydrologic Information System Server. The HIS Server is a software stack that organizes observation databases, geographic data layers, data importing and management tools, and online user interfaces such as the DASH application, into a flexible multi- tier application for serving both national-level and locally-maintained observation data. The user interface of the DASH web application allows online users to query observation networks by location and attributes, selecting stations in a user-specified area where a particular variable was measured during a given time interval. Once one or more stations and variables are selected, the user can retrieve and download the observation data for further off-line analysis. The DASH application is highly configurable. The mapping interface can be configured to display map services from multiple sources in multiple formats, including ArcGIS Server, ArcIMS, and WMS. The observation network data is configured in an XML file where you specify the network's web service location and its corresponding map layer. Upon initial deployment, two national level observation networks (USGS NWIS daily values and USGS NWIS Instantaneous values) are already pre-configured. There is also an optional login page which can be used to restrict access as well as providing a alternative to immediate downloads. For large request, users would be notified via email with a link to their data when it is ready.

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.

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu. PMID:21595965

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

Clucas, Jean; Watson, Velvin; Chancellor, Marisa K. (Technical Monitor)

1994-01-01

The Web provides new Methods for accessing Information world-wide, but the current text-and-pictures approach neither utilizes all the Web's possibilities not provides for its limitations. While the inclusion of pictures and animations in a paper communicates more effectively than text alone, It Is essentially an extension of the concept of "publication." Also, as use of the Web increases putting images and animations online will quickly load even the "Information Superhighway." We need to find forms of communication that take advantage of the special nature of the Web. This paper presents one approach: the use of the Internet and the Mosaic interface for data sharing and collaborative analysis. We will describe (and In the presentation, demonstrate) our approach: using FAST (Flow Analysis Software Toolkit), a scientific visualization package, as a data viewer and interactive tool called from MOSAIC. Our intent is to stimulate the development of other tools that utilize the unique nature of electronic communication.

Developing Interoperable Air Quality Community Portals

NASA Astrophysics Data System (ADS)

Falke, S. R.; Husar, R. B.; Yang, C. P.; Robinson, E. M.; Fialkowski, W. E.

2009-04-01

Web portals are intended to provide consolidated discovery, filtering and aggregation of content from multiple, distributed web sources targeted at particular user communities. This paper presents a standards-based information architectural approach to developing portals aimed at air quality community collaboration in data access and analysis. An important characteristic of the approach is to advance beyond the present stand-alone design of most portals to achieve interoperability with other portals and information sources. We show how using metadata standards, web services, RSS feeds and other Web 2.0 technologies, such as Yahoo! Pipes and del.icio.us, helps increase interoperability among portals. The approach is illustrated within the context of the GEOSS Architecture Implementation Pilot where an air quality community portal is being developed to provide a user interface between the portals and clearinghouse of the GEOSS Common Infrastructure and the air quality community catalog of metadata and data services.

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

How to Boost Engineering Support Via Web 2.0 - Seeds for the Ares Project...and/or Yours?

NASA Technical Reports Server (NTRS)

Scott, David W.

2010-01-01

The Mission Operations Laboratory (MOL) at Marshall Space Flight Center (MSFC) is responsible for Engineering Support capability for NASA s Ares launch system development. In pursuit of this, MOL is building the Ares Engineering and Operations Network (AEON), a web-based portal intended to provide a seamless interface to support and simplify two critical activities: a) Access and analyze Ares manufacturing, test, and flight performance data, with access to Shuttle data for comparison. b) Provide archive storage for engineering instrumentation data to support engineering design, development, and test. A mix of NASA-written and COTS software provides engineering analysis tools. A by-product of using a data portal to access and display data is access to collaborative tools inherent in a Web 2.0 environment. This paper discusses how Web 2.0 techniques, particularly social media, might be applied to the traditionally conservative and formal engineering support arena. A related paper by the author [1] considers use

Improvements to the User Interface for LHCb's Software continuous integration system.

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.; Kyriazi, S.

2015-12-01

The purpose of this paper is to identify a set of steps leading to an improved interface for LHCb's Nightly Builds Dashboard. The goal is to have an efficient application that meets the needs of both the project developers, by providing them with a user friendly interface, as well as those of the computing team supporting the system, by providing them with a dashboard allowing for better monitoring of the build job themselves. In line with what is already used by LHCb, the web interface has been implemented with the Flask Python framework for future maintainability and code clarity. The Database chosen to host the data is the schema-less CouchDB[7], serving the purpose of flexibility in document form changes. To improve the user experience, we use JavaScript libraries such as JQuery[11].

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

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.

CFGP: a web-based, comparative fungal genomics platform.

PubMed

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F; Blair, Jaime E; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

Leveraging Open Standard Interfaces in Accessing and Processing NASA Data Model Outputs

NASA Astrophysics Data System (ADS)

Falke, S. R.; Alameh, N. S.; Hoijarvi, K.; de La Beaujardiere, J.; Bambacus, M. J.

2006-12-01

An objective of NASA's Earth Science Division is to develop advanced information technologies for processing, archiving, accessing, visualizing, and communicating Earth Science data. To this end, NASA and other federal agencies have collaborated with the Open Geospatial Consortium (OGC) to research, develop, and test interoperability specifications within projects and testbeds benefiting the government, industry, and the public. This paper summarizes the results of a recent effort under the auspices of the OGC Web Services testbed phase 4 (OWS-4) to explore standardization approaches for accessing and processing the outputs of NASA models of physical phenomena. Within the OWS-4 context, experiments were designed to leverage the emerging OGC Web Processing Service (WPS) and Web Coverage Service (WCS) specifications to access, filter and manipulate the outputs of the NASA Goddard Earth Observing System (GEOS) and Goddard Chemistry Aerosol Radiation and Transport (GOCART) forecast models. In OWS-4, the intent is to provide the users with more control over the subsets of data that they can extract from the model results as well as over the final portrayal of that data. To meet that goal, experiments have been designed to test the suitability of use of OGC's Web Processing Service (WPS) and Web Coverage Service (WCS) for filtering, processing and portraying the model results (including slices by height or by time), and to identify any enhancements to the specs to meet the desired objectives. This paper summarizes the findings of the experiments highlighting the value of the Web Processing Service in providing standard interfaces for accessing and manipulating model data within spatial and temporal frameworks. The paper also points out the key shortcomings of the WPS especially in terms in comparison with a SOAP/WSDL approach towards solving the same problem.

Interactive Learning Environment: Web-based Virtual Hydrological Simulation System using Augmented and Immersive Reality

NASA Astrophysics Data System (ADS)

Demir, I.

2014-12-01

Recent developments in internet technologies make it possible to manage and visualize large data on the web. Novel visualization techniques and interactive user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The hydrological simulation system is a web-based 3D interactive learning environment for teaching hydrological processes and concepts. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create or load predefined scenarios, control environmental parameters, and evaluate environmental mitigation alternatives. The web-based simulation system provides an environment for students to learn about the hydrological processes (e.g. flooding and flood damage), and effects of development and human activity in the floodplain. The system utilizes latest web technologies and graphics processing unit (GPU) for water simulation and object collisions on the terrain. Users can access the system in three visualization modes including virtual reality, augmented reality, and immersive reality using heads-up display. The system provides various scenarios customized to fit the age and education level of various users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various visualization and interaction modes.

Focused Crawling of the Deep Web Using Service Class Descriptions

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

Rocco, D; Liu, L; Critchlow, T

2004-06-21

Dynamic Web data sources--sometimes known collectively as the Deep Web--increase the utility of the Web by providing intuitive access to data repositories anywhere that Web access is available. Deep Web services provide access to real-time information, like entertainment event listings, or present a Web interface to large databases or other data repositories. Recent studies suggest that the size and growth rate of the dynamic Web greatly exceed that of the static Web, yet dynamic content is often ignored by existing search engine indexers owing to the technical challenges that arise when attempting to search the Deep Web. To address thesemore » challenges, we present DynaBot, a service-centric crawler for discovering and clustering Deep Web sources offering dynamic content. DynaBot has three unique characteristics. First, DynaBot utilizes a service class model of the Web implemented through the construction of service class descriptions (SCDs). Second, DynaBot employs a modular, self-tuning system architecture for focused crawling of the DeepWeb using service class descriptions. Third, DynaBot incorporates methods and algorithms for efficient probing of the Deep Web and for discovering and clustering Deep Web sources and services through SCD-based service matching analysis. Our experimental results demonstrate the effectiveness of the service class discovery, probing, and matching algorithms and suggest techniques for efficiently managing service discovery in the face of the immense scale of the Deep Web.« less

Dynamic selection mechanism for quality of service aware web services

NASA Astrophysics Data System (ADS)

D'Mello, Demian Antony; Ananthanarayana, V. S.

2010-02-01

A web service is an interface of the software component that can be accessed by standard Internet protocols. The web service technology enables an application to application communication and interoperability. The increasing number of web service providers throughout the globe have produced numerous web services providing the same or similar functionality. This necessitates the use of tools and techniques to search the suitable services available over the Web. UDDI (universal description, discovery and integration) is the first initiative to find the suitable web services based on the requester's functional demands. However, the requester's requirements may also include non-functional aspects like quality of service (QoS). In this paper, the authors define a QoS model for QoS aware and business driven web service publishing and selection. The authors propose a QoS requirement format for the requesters, to specify their complex demands on QoS for the web service selection. The authors define a tree structure called quality constraint tree (QCT) to represent the requester's variety of requirements on QoS properties having varied preferences. The paper proposes a QoS broker based architecture for web service selection, which facilitates the requesters to specify their QoS requirements to select qualitatively optimal web service. A web service selection algorithm is presented, which ranks the functionally similar web services based on the degree of satisfaction of the requester's QoS requirements and preferences. The paper defines web service provider qualities to distinguish qualitatively competitive web services. The paper also presents the modelling and selection mechanism for the requester's alternative constraints defined on the QoS. The authors implement the QoS broker based system to prove the correctness of the proposed web service selection mechanism.

New Interfaces to Web Documents and Services

NASA Technical Reports Server (NTRS)

Carlisle, W. H.

1996-01-01

This paper reports on investigations into how to extend capabilities of the Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1996 Summer Faculty Fellowship program, and involved research into and prototype development of software components that provide documents and services for the World Wide Web (WWW). The WWW has become a de-facto standard for sharing resources over the internet, primarily because web browsers are freely available for the most common hardware platforms and their operating systems. As a consequence of the popularity of the internet, tools, and techniques associated with web browsers are changing rapidly. New capabilities are offered by companies that support web browsers in order to achieve or remain a dominant participant in internet services. Because a goal of the VRC is to build an environment for NASA centers, universities, and industrial partners to share information associated with Advanced Concepts Office activities, the VRC tracks new techniques and services associated with the web in order to determine the their usefulness for distributed and collaborative engineering research activities. Most recently, Java has emerged as a new tool for providing internet services. Because the major web browser providers have decided to include Java in their software, investigations into Java were conducted this summer.

Design for Connecting Spatial Data Infrastructures with Sensor Web (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; M., M.

2016-06-01

Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. It is about research to harness the sensed environment by utilizing domain specific sensor data to create a generalized sensor webframework. The challenges being semantic enablement for Spatial Data Infrastructures, and connecting the interfaces of SDI with interfaces of Sensor Web. The proposed research plan is to Identify sensor data sources, Setup an open source SDI, Match the APIs and functions between Sensor Web and SDI, and Case studies like hazard applications, urban applications etc. We take up co-operative development of SDI best practices to enable a new realm of a location enabled and semantically enriched World Wide Web - the "Geospatial Web" or "Geosemantic Web" by setting up one to one correspondence between WMS, WFS, WCS, Metadata and 'Sensor Observation Service' (SOS); 'Sensor Planning Service' (SPS); 'Sensor Alert Service' (SAS); a service that facilitates asynchronous message interchange between users and services, and between two OGC-SWE services, called the 'Web Notification Service' (WNS). Hence in conclusion, it is of importance to geospatial studies to integrate SDI with Sensor Web. The integration can be done through merging the common OGC interfaces of SDI and Sensor Web. Multi-usability studies to validate integration has to be undertaken as future research.

Semantic integration of information about orthologs and diseases: the OGO system.

PubMed

Miñarro-Gimenez, Jose Antonio; Egaña Aranguren, Mikel; Martínez Béjar, Rodrigo; Fernández-Breis, Jesualdo Tomás; Madrid, Marisa

2011-12-01

Semantic Web technologies like RDF and OWL are currently applied in life sciences to improve knowledge management by integrating disparate information. Many of the systems that perform such task, however, only offer a SPARQL query interface, which is difficult to use for life scientists. We present the OGO system, which consists of a knowledge base that integrates information of orthologous sequences and genetic diseases, providing an easy to use ontology-constrain driven query interface. Such interface allows the users to define SPARQL queries through a graphical process, therefore not requiring SPARQL expertise. Copyright © 2011 Elsevier Inc. All rights reserved.

Automation Hooks Architecture for Flexible Test Orchestration - Concept Development and Validation

NASA Technical Reports Server (NTRS)

Lansdowne, C. A.; Maclean, John R.; Winton, Chris; McCartney, Pat

2011-01-01

The Automation Hooks Architecture Trade Study for Flexible Test Orchestration sought a standardized data-driven alternative to conventional automated test programming interfaces. The study recommended composing the interface using multicast DNS (mDNS/SD) service discovery, Representational State Transfer (Restful) Web Services, and Automatic Test Markup Language (ATML). We describe additional efforts to rapidly mature the Automation Hooks Architecture candidate interface definition by validating it in a broad spectrum of applications. These activities have allowed us to further refine our concepts and provide observations directed toward objectives of economy, scalability, versatility, performance, severability, maintainability, scriptability and others.

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

The article describes the developed database designed as comprehensive data storage of the fixed target experiment BM@N [1] at Joint Institute for Nuclear Research (JINR) in Dubna. The structure and purposes of the BM@N facility will be briefly presented. The scheme of the unified database and its parameters will be described in detail. The use of the BM@N database implemented on the PostgreSQL database management system (DBMS) allows one to provide user access to the actual information of the experiment. Also the interfaces developed for the access to the database will be presented. One was implemented as the set of C++ classes to access the data without SQL statements, the other-Web-interface being available on the Web page of the BM@N experiment.

Federated Space-Time Query for Earth Science Data Using OpenSearch Conventions

NASA Astrophysics Data System (ADS)

Lynnes, C.; Beaumont, B.; Duerr, R. E.; Hua, H.

2009-12-01

The past decade has seen a burgeoning of remote sensing and Earth science data providers, as evidenced in the growth of the Earth Science Information Partner (ESIP) federation. At the same time, the need to combine diverse data sets to enable understanding of the Earth as a system has also grown. While the expansion of data providers is in general a boon to such studies, the diversity presents a challenge to finding useful data for a given study. Locating all the data files with aerosol information for a particular volcanic eruption, for example, may involve learning and using several different search tools to execute the requisite space-time queries. To address this issue, the ESIP federation is developing a federated space-time query framework, based on the OpenSearch convention (www.opensearch.org), with Geo and Time extensions. In this framework, data providers publish OpenSearch Description Documents that describe in a machine-readable form how to execute queries against the provider. The novelty of OpenSearch is that the space-time query interface becomes both machine callable and easy enough to integrate into the web browser's search box. This flexibility, together with a simple REST (HTTP-get) interface, should allow a variety of data providers to participate in the federated search framework, from large institutional data centers to individual scientists. The simple interface enables trivial querying of multiple data sources and participation in recursive-like federated searches--all using the same common OpenSearch interface. This simplicity also makes the construction of clients easy, as does existing OpenSearch client libraries in a variety of languages. Moreover, a number of clients and aggregation services already exist and OpenSearch is already supported by a number of web browsers such as Firefox and Internet Explorer.

Tripal: a construction toolkit for online genome databases.

PubMed

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

2011-01-01

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

Tripal: a construction toolkit for online genome databases

PubMed Central

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

2011-01-01

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

User Interface Composition with COTS-UI and Trading Approaches: Application for Web-Based Environmental Information Systems

NASA Astrophysics Data System (ADS)

Criado, Javier; Padilla, Nicolás; Iribarne, Luis; Asensio, Jose-Andrés

Due to the globalization of the information and knowledge society on the Internet, modern Web-based Information Systems (WIS) must be flexible and prepared to be easily accessible and manageable in real-time. In recent times it has received a special interest the globalization of information through a common vocabulary (i.e., ontologies), and the standardized way in which information is retrieved on the Web (i.e., powerful search engines, and intelligent software agents). These same principles of globalization and standardization should also be valid for the user interfaces of the WIS, but they are built on traditional development paradigms. In this paper we present an approach to reduce the gap of globalization/standardization in the generation of WIS user interfaces by using a real-time "bottom-up" composition perspective with COTS-interface components (type interface widgets) and trading services.

ECOTOX (ECOTOXICOLOGY DATABASE): AN ASSESSMENT TOOL FOR THE 21ST CENTURY

EPA Science Inventory

The ECOTOX (ECOTOXicology Database) system developed by the U.S. EPA, National Health and Environmental Effecrs Research Laboratory (NHEERL), Mid-Continent Ecology Division in Duluth, MN, (MED-Duluth), provides a web browser search interface for locating aquatic and terrestrial t...

WeBIAS: a web server for publishing bioinformatics applications.

PubMed

Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

2015-11-02

One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

A Visual Galaxy Classification Interface and its Classroom Application

NASA Astrophysics Data System (ADS)

Kautsch, Stefan J.; Phung, Chau; VanHilst, Michael; Castro, Victor H

2014-06-01

Galaxy morphology is an important topic in modern astronomy to understand questions concerning the evolution and formation of galaxies and their dark matter content. In order to engage students in exploring galaxy morphology, we developed a web-based, graphical interface that allows students to visually classify galaxy images according to various morphological types. The website is designed with HTML5, JavaScript, PHP, and a MySQL database. The classification interface provides hands-on research experience and training for students and interested clients, and allows them to contribute to studies of galaxy morphology. We present the first results of a pilot study and compare the visually classified types using our interface with that from automated classification routines.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

Establishing best practices to improve usability of web interfaces providing atmospheric data

NASA Astrophysics Data System (ADS)

Oakley, N.; Daudert, B.

2014-12-01

Accessing scientific data through an online portal can be a frustrating task. The concept of making web interfaces easy to use known as "usability" has been thoroughly researched in the field of e-commerce but has not been explicitly addressed in the atmospheric sciences. As more observation stations are installed, satellite missions flown, models run, and field campaigns performed, large amounts of data are produced. Portals on the Internet have become the favored mechanisms to share this information and are ever increasing in number. Portals are often created without being tested for usability with the target audience though the expenses of testing are low and the returns high. To remain competitive and relevant in the provision of atmospheric data, it is imperative that developers understand design elements of a successful portal to make their product stand out among others. This presentation informs the audience of the benefits and basic principles of usability for web pages presenting atmospheric data. We will also share some of the best practices and recommendations we have formulated from the results of usability testing performed on two data provision web sites hosted by the Western Regional Climate Center.

Design and development of an IoT-based web application for an intelligent remote SCADA system

NASA Astrophysics Data System (ADS)

Kao, Kuang-Chi; Chieng, Wei-Hua; Jeng, Shyr-Long

2018-03-01

This paper presents a design of an intelligent remote electrical power supervisory control and data acquisition (SCADA) system based on the Internet of Things (IoT), with Internet Information Services (IIS) for setting up web servers, an ASP.NET model-view- controller (MVC) for establishing a remote electrical power monitoring and control system by using responsive web design (RWD), and a Microsoft SQL Server as the database. With the web browser connected to the Internet, the sensing data is sent to the client by using the TCP/IP protocol, which supports mobile devices with different screen sizes. The users can provide instructions immediately without being present to check the conditions, which considerably reduces labor and time costs. The developed system incorporates a remote measuring function by using a wireless sensor network and utilizes a visual interface to make the human-machine interface (HMI) more instinctive. Moreover, it contains an analog input/output and a basic digital input/output that can be applied to a motor driver and an inverter for integration with a remote SCADA system based on IoT, and thus achieve efficient power management.

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

A RESTful interface to pseudonymization services in modern web applications.

PubMed

Lablans, Martin; Borg, Andreas; Ückert, Frank

2015-02-07

Medical research networks rely on record linkage and pseudonymization to determine which records from different sources relate to the same patient. To establish informational separation of powers, the required identifying data are redirected to a trusted third party that has, in turn, no access to medical data. This pseudonymization service receives identifying data, compares them with a list of already reported patient records and replies with a (new or existing) pseudonym. We found existing solutions to be technically outdated, complex to implement or not suitable for internet-based research infrastructures. In this article, we propose a new RESTful pseudonymization interface tailored for use in web applications accessed by modern web browsers. The interface is modelled as a resource-oriented architecture, which is based on the representational state transfer (REST) architectural style. We translated typical use-cases into resources to be manipulated with well-known HTTP verbs. Patients can be re-identified in real-time by authorized users' web browsers using temporary identifiers. We encourage the use of PID strings for pseudonyms and the EpiLink algorithm for record linkage. As a proof of concept, we developed a Java Servlet as reference implementation. The following resources have been identified: Sessions allow data associated with a client to be stored beyond a single request while still maintaining statelessness. Tokens authorize for a specified action and thus allow the delegation of authentication. Patients are identified by one or more pseudonyms and carry identifying fields. Relying on HTTP calls alone, the interface is firewall-friendly. The reference implementation has proven to be production stable. The RESTful pseudonymization interface fits the requirements of web-based scenarios and allows building applications that make pseudonymization transparent to the user using ordinary web technology. The open-source reference implementation implements the web interface as well as a scientifically grounded algorithm to generate non-speaking pseudonyms.

Web-phreeq: a WWW instructional tool for modeling the distribution of chemical species in water

NASA Astrophysics Data System (ADS)

Saini-Eidukat, Bernhardt; Yahin, Andrew

1999-05-01

A WWW-based tool, WEB-PHREEQ, was developed for classroom teaching and for routine calculation of low temperature aqueous speciation. Accessible with any computer that has an internet-connected forms-capable WWW-browser, WEB-PHREEQ provides user interface and other support for modeling, creates a properly formatted input file, passes it to the public domain program PHREEQC and returns the output to the WWW browser. Users can calculate the equilibrium speciation of a solution over a range of temperatures or can react solid minerals or gases with a particular water and examine the resulting chemistry. WEB-PHREEQ is one of a number of interactive distributed-computing programs available on the WWW that are of interest to geoscientists.

SWE-based Observation Data Delivery from the Instrument to the User - Sensor Web Technology in the NeXOS Project

NASA Astrophysics Data System (ADS)

Jirka, Simon; del Rio, Joaquin; Toma, Daniel; Martinez, Enoc; Delory, Eric; Pearlman, Jay; Rieke, Matthes; Stasch, Christoph

2017-04-01

The rapidly evolving technology for building Web-based (spatial) information infrastructures and Sensor Webs, there are new opportunities to improve the process how ocean data is collected and managed. A central element in this development is the suite of Sensor Web Enablement (SWE) standards specified by the Open Geospatial Consortium (OGC). This framework of standards comprises on the one hand data models as well as formats for measurement data (ISO/OGC Observations and Measurement, O&M) and metadata describing measurement processes and sensors (OGC Sensor Model Language, SensorML). On the other hand the SWE standards comprise (Web service) interface specifications for pull-based access to observation data (OGC Sensor Observation Service, SOS) and for controlling or configuring sensors (OGC Sensor Planning Service, SPS). Also within the European INSPIRE framework the SWE standards play an important role as the SOS is the recommended download service interface for O&M-encoded observation data sets. In the context of the EU-funded Oceans of Tomorrow initiative the NeXOS (Next generation, Cost-effective, Compact, Multifunctional Web Enabled Ocean Sensor Systems Empowering Marine, Maritime and Fisheries Management) project is developing a new generation of in-situ sensors that make use of the SWE standards to facilitate the data publication process and the integration into Web based information infrastructures. This includes the development of a dedicated firmware for instruments and sensor platforms (SEISI, Smart Electronic Interface for Sensors and Instruments) maintained by the Universitat Politècnica de Catalunya (UPC). Among other features, SEISI makes use of OGC SWE standards such OGC-PUCK, to enable a plug-and-play mechanism for sensors based on SensorML encoded metadata. Thus, if a new instrument is attached to a SEISI-based platform, it automatically configures the connection to these instruments, automatically generated data files compliant with the ISO/OGC Observations and Measurements standard and initiates the data transmission into the NeXOS Sensor Web infrastructure. Besides these platform-related developments, NeXOS has realised the full path of data transmission from the sensor to the end user application. The conceptual architecture design is implemented by a series of open source SWE software packages provided by 52°North. This comprises especially different SWE server components (i.e. OGC Sensor Observation Service), tools for data visualisation (e.g. the 52°North Helgoland SOS viewer), and an editor for providing SensorML-based metadata (52°North smle). As a result, NeXOS has demonstrated how the SWE standards help to improve marine observation data collection. Within this presentation, we will present the experiences and findings of the NeXOS project and will provide recommendation for future work directions.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

NGL Viewer: a web application for molecular visualization.

PubMed

Rose, Alexander S; Hildebrand, Peter W

2015-07-01

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

Mfold web server for nucleic acid folding and hybridization prediction.

PubMed

Zuker, Michael

2003-07-01

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.

Web Navigation Sequences Automation in Modern Websites

NASA Astrophysics Data System (ADS)

Montoto, Paula; Pan, Alberto; Raposo, Juan; Bellas, Fernando; López, Javier

Most today’s web sources are designed to be used by humans, but they do not provide suitable interfaces for software programs. That is why a growing interest has arisen in so-called web automation applications that are widely used for different purposes such as B2B integration, automated testing of web applications or technology and business watch. Previous proposals assume models for generating and reproducing navigation sequences that are not able to correctly deal with new websites using technologies such as AJAX: on one hand existing systems only allow recording simple navigation actions and, on the other hand, they are unable to detect the end of the effects caused by an user action. In this paper, we propose a set of new techniques to record and execute web navigation sequences able to deal with all the complexity existing in AJAX-based web sites. We also present an exhaustive evaluation of the proposed techniques that shows very promising results.

VisGets: coordinated visualizations for web-based information exploration and discovery.

PubMed

Dörk, Marian; Carpendale, Sheelagh; Collins, Christopher; Williamson, Carey

2008-01-01

In common Web-based search interfaces, it can be difficult to formulate queries that simultaneously combine temporal, spatial, and topical data filters. We investigate how coordinated visualizations can enhance search and exploration of information on the World Wide Web by easing the formulation of these types of queries. Drawing from visual information seeking and exploratory search, we introduce VisGets--interactive query visualizations of Web-based information that operate with online information within a Web browser. VisGets provide the information seeker with visual overviews of Web resources and offer a way to visually filter the data. Our goal is to facilitate the construction of dynamic search queries that combine filters from more than one data dimension. We present a prototype information exploration system featuring three linked VisGets (temporal, spatial, and topical), and used it to visually explore news items from online RSS feeds.

How to Display Hazards and other Scientific Data Using Google Maps

NASA Astrophysics Data System (ADS)

Venezky, D. Y.; Fee, J. M.

2007-12-01

The U.S. Geological Survey's (USGS) Volcano Hazard Program (VHP) is launching a map-based interface to display hazards information using the Google® Map API (Application Program Interface). Map-based interfaces provide a synoptic view of data, making patterns easier to detect and allowing users to quickly ascertain where hazards are in relation to major population and infrastructure centers. Several map-based interfaces are now simple to run on a web server, providing ideal platforms for sharing information with colleagues, emergency managers, and the public. There are three main steps to making data accessible on a map-based interface; formatting the input data, plotting the data on the map, and customizing the user interface. The presentation, "Creating Geospatial RSS and ATOM feeds for Map-based Interfaces" (Fee and Venezky, this session), reviews key features for map input data. Join us for this presentation on how to plot data in a geographic context and then format the display with images, custom markers, and links to external data. Examples will show how the VHP Volcano Status Map was created and how to plot a field trip with driving directions.

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

PubMed

Swertz, Morris A; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K; Kanterakis, Alexandros; Roos, Erik T; Lops, Joris; Thorisson, Gudmundur A; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J; de Brock, Engbert O; Jansen, Ritsert C; Parkinson, Helen

2010-12-21

There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

Moon Trek: An Interactive Web Portal for Current and Future Lunar Missions

NASA Technical Reports Server (NTRS)

Day, B; Law, Emily S.

2017-01-01

NASA's Moon Trek (https://moontrek.jpl.nasa.gov) is the successor to and replacement for NASA's Lunar Mapping and Modeling Portal (LMMP). Released in 2017, Moon Trek features a new interface with improved ways to access, visualize, and analyze data. Moon Trek provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions.

Moon Trek: An Interactive Web Portal for Current and Future Lunar Missions

NASA Astrophysics Data System (ADS)

Day, B.; Law, E.

2017-09-01

NASA's Moon Trek (https://moontrek.jpl.nasa.gov) is the successor to and replacement for NASA's Lunar Mapping and Modeling Portal (LMMP). Released in 2017, Moon Trek features a new interface with improved ways to access, visualize, and analyse data. Moon Trek provides a web-based Portal and a suite of interactive visualization and analysis tools to enable mission planners, lunar scientists, and engineers to access mapped lunar data products from past and current lunar missions.

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth

PubMed Central

2014-01-01

Abstract The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface. In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements. We have shown that it is possible to successfully integrate large amounts of descriptive biodiversity data from diverse sources into a robust, standards-based, dynamic, and scalable infrastructure. Increasing global participation and the emergence of EOL-powered applications demonstrate that EOL is becoming a significant resource for anyone interested in biological diversity. PMID:24891832

Dcs Data Viewer, an Application that Accesses ATLAS DCS Historical Data

NASA Astrophysics Data System (ADS)

Tsarouchas, C.; Schlenker, S.; Dimitrov, G.; Jahn, G.

2014-06-01

The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. The Detector Control System (DCS) of ATLAS is responsible for the supervision of the detector equipment, the reading of operational parameters, the propagation of the alarms and the archiving of important operational data in a relational database (DB). DCS Data Viewer (DDV) is an application that provides access to the ATLAS DCS historical data through a web interface. Its design is structured using a client-server architecture. The pythonic server connects to the DB and fetches the data by using optimized SQL requests. It communicates with the outside world, by accepting HTTP requests and it can be used stand alone. The client is an AJAX (Asynchronous JavaScript and XML) interactive web application developed under the Google Web Toolkit (GWT) framework. Its web interface is user friendly, platform and browser independent. The selection of metadata is done via a column-tree view or with a powerful search engine. The final visualization of the data is done using java applets or java script applications as plugins. The default output is a value-over-time chart, but other types of outputs like tables, ascii or ROOT files are supported too. Excessive access or malicious use of the database is prevented by a dedicated protection mechanism, allowing the exposure of the tool to hundreds of inexperienced users. The current configuration of the client and of the outputs can be saved in an XML file. Protection against web security attacks is foreseen and authentication constrains have been taken into account, allowing the exposure of the tool to hundreds of users world wide. Due to its flexible interface and its generic and modular approach, DDV could be easily used for other experiment control systems.

UIVerify: A Web-Based Tool for Verification and Automatic Generation of User Interfaces

NASA Technical Reports Server (NTRS)

Shiffman, Smadar; Degani, Asaf; Heymann, Michael

2004-01-01

In this poster, we describe a web-based tool for verification and automatic generation of user interfaces. The verification component of the tool accepts as input a model of a machine and a model of its interface, and checks that the interface is adequate (correct). The generation component of the tool accepts a model of a given machine and the user's task, and then generates a correct and succinct interface. This write-up will demonstrate the usefulness of the tool by verifying the correctness of a user interface to a flight-control system. The poster will include two more examples of using the tool: verification of the interface to an espresso machine, and automatic generation of a succinct interface to a large hypothetical machine.

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

Molray--a web interface between O and the POV-Ray ray tracer.

PubMed

Harris, M; Jones, T A

2001-08-01

A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110-119]. The interface allows the user to select O-plot files and set parameters to create standard input files for the popular ray-tracing renderer POV-Ray, which can then produce publication-quality still images or simple movies. To ensure ease of use, we have made this service available to the O user community via the World Wide Web. The public Molray server is available at http://xray.bmc.uu.se/molray.

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

NASA Astrophysics Data System (ADS)

Huang, L. Xinglai; Sheng, Grant

2006-10-01

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

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.

SAFOD Brittle Microstructure and Mechanics Knowledge Base (BM2KB)

NASA Astrophysics Data System (ADS)

Babaie, Hassan A.; Broda Cindi, M.; Hadizadeh, Jafar; Kumar, Anuj

2013-07-01

Scientific drilling near Parkfield, California has established the San Andreas Fault Observatory at Depth (SAFOD), which provides the solid earth community with short range geophysical and fault zone material data. The BM2KB ontology was developed in order to formalize the knowledge about brittle microstructures in the fault rocks sampled from the SAFOD cores. A knowledge base, instantiated from this domain ontology, stores and presents the observed microstructural and analytical data with respect to implications for brittle deformation and mechanics of faulting. These data can be searched on the knowledge base‧s Web interface by selecting a set of terms (classes, properties) from different drop-down lists that are dynamically populated from the ontology. In addition to this general search, a query can also be conducted to view data contributed by a specific investigator. A search by sample is done using the EarthScope SAFOD Core Viewer that allows a user to locate samples on high resolution images of core sections belonging to different runs and holes. The class hierarchy of the BM2KB ontology was initially designed using the Unified Modeling Language (UML), which was used as a visual guide to develop the ontology in OWL applying the Protégé ontology editor. Various Semantic Web technologies such as the RDF, RDFS, and OWL ontology languages, SPARQL query language, and Pellet reasoning engine, were used to develop the ontology. An interactive Web application interface was developed through Jena, a java based framework, with AJAX technology, jsp pages, and java servlets, and deployed via an Apache tomcat server. The interface allows the registered user to submit data related to their research on a sample of the SAFOD core. The submitted data, after initial review by the knowledge base administrator, are added to the extensible knowledge base and become available in subsequent queries to all types of users. The interface facilitates inference capabilities in the ontology, supports SPARQL queries, allows for modifications based on successive discoveries, and provides an accessible knowledge base on the Web.

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species

PubMed Central

Kumar, Sujai; Stevens, Lewis; Blaxter, Mark

2017-01-01

Abstract As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive application programming interface. Here we introduce GenomeHubs, which provide a containerized environment to facilitate the setup and hosting of custom Ensembl genome browsers. This simplifies mirroring of existing content and import of new genomic data into the Ensembl database schema. GenomeHubs also provide a set of analysis containers to decorate imported genomes with results of standard analyses and functional annotations and support export to flat files, including EMBL format for submission of assemblies and annotations to International Nucleotide Sequence Database Collaboration. Database URL: http://GenomeHubs.org PMID:28605774

Power User Interface

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe

2006-01-01

Power User Interface 5.0 (PUI) is a system of middleware, written for expert users in the Earth-science community, PUI enables expedited ordering of data granules on the basis of specific granule-identifying information that the users already know or can assemble. PUI also enables expert users to perform quick searches for orderablegranule information for use in preparing orders. PUI 5.0 is available in two versions (note: PUI 6.0 has command-line mode only): a Web-based application program and a UNIX command-line- mode client program. Both versions include modules that perform data-granule-ordering functions in conjunction with external systems. The Web-based version works with Earth Observing System Clearing House (ECHO) metadata catalog and order-entry services and with an open-source order-service broker server component, called the Mercury Shopping Cart, that is provided separately by Oak Ridge National Laboratory through the Department of Energy. The command-line version works with the ECHO metadata and order-entry process service. Both versions of PUI ultimately use ECHO to process an order to be sent to a data provider. Ordered data are provided through means outside the PUI software system.

Local intelligent electronic device (IED) rendering templates over limited bandwidth communication link to manage remote IED

DOEpatents

Bradetich, Ryan; Dearien, Jason A; Grussling, Barry Jakob; Remaley, Gavin

2013-11-05

The present disclosure provides systems and methods for remote device management. According to various embodiments, a local intelligent electronic device (IED) may be in communication with a remote IED via a limited bandwidth communication link, such as a serial link. The limited bandwidth communication link may not support traditional remote management interfaces. According to one embodiment, a local IED may present an operator with a management interface for a remote IED by rendering locally stored templates. The local IED may render the locally stored templates using sparse data obtained from the remote IED. According to various embodiments, the management interface may be a web client interface and/or an HTML interface. The bandwidth required to present a remote management interface may be significantly reduced by rendering locally stored templates rather than requesting an entire management interface from the remote IED. According to various embodiments, an IED may comprise an encryption transceiver.

Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

This paper discusses the detailed design of an XML databinding framework for aircraft engine simulation. The framework provides an object interface to access and use engine data. while at the same time preserving the meaning of the original data. The Language independent representation of engine component data enables users to move around XML data using HTTP through disparate networks. The application of this framework is demonstrated via a web-based turbofan propulsion system simulation using the World Wide Web (WWW). A Java Servlet based web component architecture is used for rendering XML engine data into HTML format and dealing with input events from the user, which allows users to interact with simulation data from a web browser. The simulation data can also be saved to a local disk for archiving or to restart the simulation at a later time.

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

PubMed Central

2010-01-01

Background AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. Methods The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. Results We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. Conclusions The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine. PMID:20977768

Development of Web Interfaces for Analysis Codes

NASA Astrophysics Data System (ADS)

Emoto, M.; Watanabe, T.; Funaba, H.; Murakami, S.; Nagayama, Y.; Kawahata, K.

Several codes have been developed to analyze plasma physics. However, most of them are developed to run on supercomputers. Therefore, users who typically use personal computers (PCs) find it difficult to use these codes. In order to facilitate the widespread use of these codes, a user-friendly interface is required. The authors propose Web interfaces for these codes. To demonstrate the usefulness of this approach, the authors developed Web interfaces for two analysis codes. One of them is for FIT developed by Murakami. This code is used to analyze the NBI heat deposition, etc. Because it requires electron density profiles, electron temperatures, and ion temperatures as polynomial expressions, those unfamiliar with the experiments find it difficult to use this code, especially visitors from other institutes. The second one is for visualizing the lines of force in the LHD (large helical device) developed by Watanabe. This code is used to analyze the interference caused by the lines of force resulting from the various structures installed in the vacuum vessel of the LHD. This code runs on PCs; however, it requires that the necessary parameters be edited manually. Using these Web interfaces, users can execute these codes interactively.

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

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

web cellHTS2: a web-application for the analysis of high-throughput screening data.

PubMed

Pelz, Oliver; Gilsdorf, Moritz; Boutros, Michael

2010-04-12

The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2. The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats. The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.

Marine Web Portal as an Interface between Users and Marine Data and Information Sources

NASA Astrophysics Data System (ADS)

Palazov, A.; Stefanov, A.; Marinova, V.; Slabakova, V.

2012-04-01

Fundamental elements of the success of marine data and information management system and an effective support of marine and maritime economic activities are the speed and the ease with which users can identify, locate, get access, exchange and use oceanographic and marine data and information. There are a lot of activities and bodies have been identified as marine data and information users, such as: science, government and local authorities, port authorities, shipping, marine industry, fishery and aquaculture, tourist industry, environmental protection, coast protection, oil spills combat, Search and Rescue, national security, civil protection, and general public. On other hand diverse sources of real-time and historical marine data and information exist and generally they are fragmented, distributed in different places and sometimes unknown for the users. The marine web portal concept is to build common web based interface which will provide users fast and easy access to all available marine data and information sources, both historical and real-time such as: marine data bases, observing systems, forecasting systems, atlases etc. The service is regionally oriented to meet user needs. The main advantage of the portal is that it provides general look "at glance" on all available marine data and information as well as direct user to easy discover data and information in interest. It is planned to provide personalization ability, which will give the user instrument to tailor visualization according its personal needs.

Web tools for predictive toxicology model building.

PubMed

Jeliazkova, Nina

2012-07-01

The development and use of web tools in chemistry has accumulated more than 15 years of history already. Powered by the advances in the Internet technologies, the current generation of web systems are starting to expand into areas, traditional for desktop applications. The web platforms integrate data storage, cheminformatics and data analysis tools. The ease of use and the collaborative potential of the web is compelling, despite the challenges. The topic of this review is a set of recently published web tools that facilitate predictive toxicology model building. The focus is on software platforms, offering web access to chemical structure-based methods, although some of the frameworks could also provide bioinformatics or hybrid data analysis functionalities. A number of historical and current developments are cited. In order to provide comparable assessment, the following characteristics are considered: support for workflows, descriptor calculations, visualization, modeling algorithms, data management and data sharing capabilities, availability of GUI or programmatic access and implementation details. The success of the Web is largely due to its highly decentralized, yet sufficiently interoperable model for information access. The expected future convergence between cheminformatics and bioinformatics databases provides new challenges toward management and analysis of large data sets. The web tools in predictive toxicology will likely continue to evolve toward the right mix of flexibility, performance, scalability, interoperability, sets of unique features offered, friendly user interfaces, programmatic access for advanced users, platform independence, results reproducibility, curation and crowdsourcing utilities, collaborative sharing and secure access.

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…

Publication, discovery and interoperability of Clinical Decision Support Systems: A Linked Data approach.

PubMed

Marco-Ruiz, Luis; Pedrinaci, Carlos; Maldonado, J A; Panziera, Luca; Chen, Rong; Bellika, J Gustav

2016-08-01

The high costs involved in the development of Clinical Decision Support Systems (CDSS) make it necessary to share their functionality across different systems and organizations. Service Oriented Architectures (SOA) have been proposed to allow reusing CDSS by encapsulating them in a Web service. However, strong barriers in sharing CDS functionality are still present as a consequence of lack of expressiveness of services' interfaces. Linked Services are the evolution of the Semantic Web Services paradigm to process Linked Data. They aim to provide semantic descriptions over SOA implementations to overcome the limitations derived from the syntactic nature of Web services technologies. To facilitate the publication, discovery and interoperability of CDS services by evolving them into Linked Services that expose their interfaces as Linked Data. We developed methods and models to enhance CDS SOA as Linked Services that define a rich semantic layer based on machine interpretable ontologies that powers their interoperability and reuse. These ontologies provided unambiguous descriptions of CDS services properties to expose them to the Web of Data. We developed models compliant with Linked Data principles to create a semantic representation of the components that compose CDS services. To evaluate our approach we implemented a set of CDS Linked Services using a Web service definition ontology. The definitions of Web services were linked to the models developed in order to attach unambiguous semantics to the service components. All models were bound to SNOMED-CT and public ontologies (e.g. Dublin Core) in order to count on a lingua franca to explore them. Discovery and analysis of CDS services based on machine interpretable models was performed reasoning over the ontologies built. Linked Services can be used effectively to expose CDS services to the Web of Data by building on current CDS standards. This allows building shared Linked Knowledge Bases to provide machine interpretable semantics to the CDS service description alleviating the challenges on interoperability and reuse. Linked Services allow for building 'digital libraries' of distributed CDS services that can be hosted and maintained in different organizations. Copyright © 2016 Elsevier Inc. All rights reserved.

Integrated system for remotely monitoring critical physiological parameters

NASA Astrophysics Data System (ADS)

Alexakis, S.; Karalis, S.; Asvestas, P.

2015-09-01

Monitoring several human parameters (temperature, heart rate, blood pressure etc.) is an essential task in health care in hospitals as well as in home care. This paper presents the design and implementation of an integrated, embedded system that includes an electrocardiograph of nine leads and two channels, a digital thermometer for measuring the body temperature and a power supply. The system provides networking capabilities (wired or wireless) and is accessible by means of a web interface that allows the user to select the leads, as well as to review the values of heart rate (beats per minute) and body temperature. Furthermore, there is the option of saving all the data in a Micro SD memory card or in a Google Spreadsheet. The necessary analog circuits for signal conditioning (amplification and filtering) were manufactured on printed circuit boards (PCB). The system was built around Arduino Yun, which is a platform that contains a microcontroller and a microprocessor running a special LINUX distribution. Furthermore, the Arduino Yun provides the necessary network connectivity capabilities by means of the integrated Wi-Fi and Ethernet interfaces. The web interface was developed using HTML pages with JavaScript support. The system was tested on simulated data as well as real data, providing satisfactory accuracy regarding the measurement of the heart rate (±3 bpm error) and the temperature (±0.3°C error).

Migrating Department of Defense (DoD) Web Service Based Applications to Mobile Computing Platforms

DTIC Science & Technology

2012-03-01

World Wide Web Consortium (W3C) Geolocation API to identify the device’s location and then center the map on the device. Finally, we modify the entry...THIS PAGE INTENTIONALLY LEFT BLANK xii List of Acronyms and Abbreviations API Application Programming Interface CSS Cascading Style Sheets CLIMO...Java API for XML Web Services Reference Implementation JS JavaScript JSNI JavaScript Native Interface METOC Meteorological and Oceanographic MAA Mobile

Development of XML Schema for Broadband Digital Seismograms and Data Center Portal

NASA Astrophysics Data System (ADS)

Takeuchi, N.; Tsuboi, S.; Ishihara, Y.; Nagao, H.; Yamagishi, Y.; Watanabe, T.; Yanaka, H.; Yamaji, H.

2008-12-01

There are a number of data centers around the globe, where the digital broadband seismograms are opened to researchers. Those centers use their own user interfaces and there are no standard to access and retrieve seismograms from different data centers using unified interface. One of the emergent technologies to realize unified user interface for different data centers is the concept of WebService and WebService portal. Here we have developed a prototype of data center portal for digital broadband seismograms. This WebService portal uses WSDL (Web Services Description Language) to accommodate differences among the different data centers. By using the WSDL, alteration and addition of data center user interfaces can be easily managed. This portal, called NINJA Portal, assumes three WebServices: (1) database Query service, (2) Seismic event data request service, and (3) Seismic continuous data request service. Current system supports both station search of database Query service and seismic continuous data request service. Data centers supported by this NINJA portal will be OHP data center in ERI and Pacific21 data center in IFREE/JAMSTEC in the beginning. We have developed metadata standard for seismological data based on QuakeML for parametric data, which has been developed by ETH Zurich, and XML-SEED for waveform data, which was developed by IFREE/JAMSTEC. The prototype of NINJA portal is now released through IFREE web page (http://www.jamstec.go.jp/pacific21/).

Sign language Web pages.

PubMed

Fels, Deborah I; Richards, Jan; Hardman, Jim; Lee, Daniel G

2006-01-01

The WORLD WIDE WEB has changed the way people interact. It has also become an important equalizer of information access for many social sectors. However, for many people, including some sign language users, Web accessing can be difficult. For some, it not only presents another barrier to overcome but has left them without cultural equality. The present article describes a system that allows sign language-only Web pages to be created and linked through a video-based technique called sign-linking. In two studies, 14 Deaf participants examined two iterations of signlinked Web pages to gauge the usability and learnability of a signing Web page interface. The first study indicated that signing Web pages were usable by sign language users but that some interface features required improvement. The second study showed increased usability for those features; users consequently couldnavigate sign language information with ease and pleasure.

Protecting clinical data on Web client computers: the PCASSO approach.

PubMed Central

Masys, D. R.; Baker, D. B.

1998-01-01

The ubiquity and ease of use of the Web have made it an increasingly popular medium for communication of health-related information. Web interfaces to commercially available clinical information systems are now available or under development by most major vendors. To the extent that such interfaces involve the use of unprotected operating systems, they are vulnerable to security limitations of Web client software environments. The Patient Centered Access to Secure Systems Online (PCASSO) project extends the protections for person-identifiable health data on Web client computers. PCASSO uses several approaches, including physical protection of authentication information, execution containment, graphical displays, and monitoring the client system for intrusions and co-existing programs that may compromise security. PMID:9929243

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

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.

PubMed

Neugebauer, Tomasz; Bordeleau, Eric; Burrus, Vincent; Brzezinski, Ryszard

2015-01-01

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

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

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

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

Distribution of guidance models for cardiac resynchronization therapy in the setting of multi-center clinical trials

NASA Astrophysics Data System (ADS)

Rajchl, Martin; Abhari, Kamyar; Stirrat, John; Ukwatta, Eranga; Cantor, Diego; Li, Feng P.; Peters, Terry M.; White, James A.

2014-03-01

Multi-center trials provide the unique ability to investigate novel techniques across a range of geographical sites with sufficient statistical power, the inclusion of multiple operators determining feasibility under a wider array of clinical environments and work-flows. For this purpose, we introduce a new means of distributing pre-procedural cardiac models for image-guided interventions across a large scale multi-center trial. In this method, a single core facility is responsible for image processing, employing a novel web-based interface for model visualization and distribution. The requirements for such an interface, being WebGL-based, are minimal and well within the realms of accessibility for participating centers. We then demonstrate the accuracy of our approach using a single-center pacemaker lead implantation trial with generic planning models.

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).

G4RNA screener web server: User focused interface for RNA G-quadruplex prediction.

PubMed

Garant, Jean-Michel; Perreault, Jean-Pierre; Scott, Michelle S

2018-06-06

Though RNA G-quadruplexes became a focus of study over a decade ago, the main challenge associated with the identification of new potential G-quadruplexes remains a bottleneck step. It slows the study of these non-canonical structures in nucleic acids, and thus the understanding of their significance. The G4RNA screener is an accurate tool for the prediction of RNA G-quadruplexes but its deployment has brought to light an issue with its accessibility to G-quadruplex experts and biologists. G4RNA screener web server is a platform that provides a much needed interface to manage the input, parameters and result display of the main command-line ready tool. It is accessible at http://scottgroup.med.usherbrooke.ca/G4RNA_screener/. Copyright © 2018. Published by Elsevier B.V.

Usage and User Acceptance of Applied Physics Letters Online

NASA Astrophysics Data System (ADS)

Ingoldsby, Timothy C.

1996-03-01

Applied Physics Letters Online became the first established physics print journal to appear online in full-text, hyperlinked form effective with January 1996 issues. In partnership with the Online Computer Library Center (OCLC), APL Online at the same time became the first established scientific or engineering journal to appear on the World Wide Web, in addition to being available through OCLC's proprietary Guidon user interface. AIP has now accumulated usage data for more than one year of operation, and has recently completed a survey of its full subscriber base. Usage has steadily increased throughout the year, with subscribers showing a clear preference for the Web version, even though it provides an interface in many ways inferior to OCLC's Guidon. Usage data and subscriber survey results will be presented, and directions for future research in online information delivery will be presented.

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

PubMed Central

2004-01-01

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

Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface.

PubMed

Weidlich, Iwona E; Pevzner, Yuri; Miller, Benjamin T; Filippov, Igor V; Woodcock, H Lee; Brooks, Bernard R

2015-01-05

Recent availability of large publicly accessible databases of chemical compounds and their biological activities (PubChem, ChEMBL) has inspired us to develop a web-based tool for structure activity relationship and quantitative structure activity relationship modeling to add to the services provided by CHARMMing (www.charmming.org). This new module implements some of the most recent advances in modern machine learning algorithms-Random Forest, Support Vector Machine, Stochastic Gradient Descent, Gradient Tree Boosting, so forth. A user can import training data from Pubchem Bioassay data collections directly from our interface or upload his or her own SD files which contain structures and activity information to create new models (either categorical or numerical). A user can then track the model generation process and run models on new data to predict activity. © 2014 Wiley Periodicals, Inc.

COLE: A Web-based Tool for Interfacing with Forest Inventory Data

Treesearch

Patrick Proctor; Linda S. Heath; Paul C. Van Deusen; Jeffery H. Gove; James E. Smith

2005-01-01

We are developing an online computer program to provide forest carbon related estimates for the conterminous United States (COLE). Version 1.0 of the program features carbon estimates based on data from the USDA Forest Service Eastwide Forest Inventory database. The program allows the user to designate an area of interest, and currently provides area, growing-stock...

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

PubMed

Konc, Janez; Janezic, Dusanka

2012-07-01

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

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

PubMed Central

Konc, Janez; Janežič, Dušanka

2012-01-01

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

BeefTracker: Spatial Tracking and Geodatabase for Beef Herd Sustainability and Lifecycle Analysis

NASA Astrophysics Data System (ADS)

Oltjen, J. W.; Stackhouse, J.; Forero, L.; Stackhouse-Lawson, K.

2015-12-01

We have developed a web-based mapping platform named "BeefTracker" to provide beef cattle ranchers a tool to determine how cattle production fits within sustainable ecosystems and to provide regional data to update beef sustainability lifecycle analysis. After initial identification and mapping of pastures, herd data (class and number of animals) are input on a mobile device in the field with a graphical pasture interface, stored in the cloud, and linked via the web to a personal computer for inventory tracking and analysis. Pasture use calculated on an animal basis provides quantifiable data regarding carrying capacity and subsequent beef production to provide more accurate data inputs for beef sustainability lifecycle analysis. After initial testing by university range scientists and ranchers we have enhanced the BeefTracker application to work when cell service is unavailable and to improve automation for increased ease of use. Thus far experiences with BeefTracker have been largely positive, due to livestock producers' perception of the need for this type of software application and its intuitive interface. We are now in the process of education to increase its use throughout the U.S.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Sand, Olivier; Janky, Rekin's; Vanderstocken, Gilles; Deville, Yves; van Helden, Jacques

2008-07-01

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

PubMed Central

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

The Physiology Constant Database of Teen-Agers in Beijing

PubMed Central

Wei-Qi, Wei; Guang-Jin, Zhu; Cheng-Li, Xu; Shao-Mei, Han; Bao-Shen, Qi; Li, Chen; Shu-Yu, Zu; Xiao-Mei, Zhou; Wen-Feng, Hu; Zheng-Guo, Zhang

2004-01-01

Physiology constants of adolescents are important to understand growing living systems and are a useful reference in clinical and epidemiological research. Until recently, physiology constants were not available in China and therefore most physiologists, physicians, and nutritionists had to use data from abroad for reference. However, the very difference between the Eastern and Western races casts doubt on the usefulness of overseas data. We have therefore created a database system to provide a repository for the storage of physiology constants of teen-agers in Beijing. The several thousands of pieces of data are now divided into hematological biochemistry, lung function, and cardiac function with all data manually checked before being transferred into the database. The database was accomplished through the development of a web interface, scripts, and a relational database. The physiology data were integrated into the relational database system to provide flexible facilities by using combinations of various terms and parameters. A web browser interface was designed for the users to facilitate their searching. The database is available on the web. The statistical table, scatter diagram, and histogram of the data are available for both anonym and user according to queries, while only the user can achieve detail, including download data and advanced search. PMID:15258669

UManSysProp: an online facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, D.; Barley, M. H.; Bane, M.; Higham, N.; Aumont, B.; McFiggans, G.

2015-11-01

In this paper we describe the development and application of a new web based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include: pure component vapour pressures, critical properties and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN activation potential of mixed inorganic/organic aerosol particles; absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES strings and UManSysProp will automatically extract the relevant information for calculations. Built using open source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web-interface, or can be accessed using the user's own code via a JSON API. In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

Opal web services for biomedical applications.

PubMed

Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

2010-07-01

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

User-Friendly Interface Developed for a Web-Based Service for SpaceCAL Emulations

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

A team at the NASA Glenn Research Center is developing a Space Communications Architecture Laboratory (SpaceCAL) for protocol development activities for coordinated satellite missions. SpaceCAL will provide a multiuser, distributed system to emulate space-based Internet architectures, backbone networks, formation clusters, and constellations. As part of a new effort in 2003, building blocks are being defined for an open distributed system to make the satellite emulation test bed accessible through an Internet connection. The first step in creating a Web-based service to control the emulation remotely is providing a user-friendly interface for encoding the data into a well-formed and complete Extensible Markup Language (XML) document. XML provides coding that allows data to be transferred between dissimilar systems. Scenario specifications include control parameters, network routes, interface bandwidths, delay, and bit error rate. Specifications for all satellite, instruments, and ground stations in a given scenario are also included in the XML document. For the SpaceCAL emulation, the XML document can be created using XForms, a Webbased forms language for data collection. Contrary to older forms technology, the interactive user interface makes the science prevalent, not the data representation. Required versus optional input fields, default values, automatic calculations, data validation, and reuse will help researchers quickly and accurately define missions. XForms can apply any XML schema defined for the test mission to validate data before forwarding it to the emulation facility. New instrument definitions, facilities, and mission types can be added to the existing schema. The first prototype user interface incorporates components for interactive input and form processing. Internet address, data rate, and the location of the facility are implemented with basic form controls with default values provided for convenience and efficiency using basic XForms operations. Because different emulation scenarios will vary widely in their component structure, more complex operations are used to add and delete facilities.

A RESTful API for accessing microbial community data for MG-RAST

DOE PAGES

Wilke, Andreas; Bischof, Jared; Harrison, Travis; ...

2015-01-08

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, asmore » well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http:// kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase’s microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.« less

A RESTful API for Accessing Microbial Community Data for MG-RAST

PubMed Central

Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M.; Desai, Narayan; Meyer, Folker

2015-01-01

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service. PMID:25569221

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

PubMed

Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-07-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

PubMed Central

Krüger, Dennis M.; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-01-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement. PMID:23609541

EarthServer2 : The Marine Data Service - Web based and Programmatic Access to Ocean Colour Open Data

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter

2017-04-01

The ESA Ocean Colour - Climate Change Initiative (ESA OC-CCI) has produced a long-term high quality global dataset with associated per-pixel uncertainty data. This dataset has now grown to several hundred terabytes (uncompressed) and is freely available to download. However, the sheer size of the dataset can act as a barrier to many users; large network bandwidth, local storage and processing requirements can prevent researchers without the backing of a large organisation from taking advantage of this raw data. The EC H2020 project, EarthServer2, aims to create a federated data service providing access to more than 1 petabyte of earth science data. Within this federation the Marine Data Service already provides an innovative on-line tool-kit for filtering, analysing and visualising OC-CCI data. Data are made available, filtered and processed at source through a standards-based interface, the Open Geospatial Consortium Web Coverage Service and Web Coverage Processing Service. This work was initiated in the EC FP7 EarthServer project where it was found that the unfamiliarity and complexity of these interfaces itself created a barrier to wider uptake. The continuation project, EarthServer2, addresses these issues by providing higher level tools for working with these data. We will present some examples of these tools. Many researchers wish to extract time series data from discrete points of interest. We will present a web based interface, based on NASA/ESA WebWorldWind, for selecting points of interest and plotting time series from a chosen dataset. In addition, a CSV file of locations and times, such as a ship's track, can be uploaded and these points extracted and returned in a CSV file allowing researchers to work with the extract locally, such as a spreadsheet. We will also present a set of Python and JavaScript APIs that have been created to complement and extend the web based GUI. These APIs allow the selection of single points and areas for extraction. The extracted data is returned as structured data (for instance a Python array) which can then be passed directly to local processing code. We will highlight how the libraries can be used by the community and integrated into existing systems, for instance by the use of Jupyter notebooks to share Python code examples which can then be used by other researchers as a basis for their own work.

Multimedia data repository for the World Wide Web

NASA Astrophysics Data System (ADS)

Chen, Ken; Lu, Dajin; Xu, Duanyi

1998-08-01

This paper introduces the design and implementation of a Multimedia Data Repository served as a multimedia information system, which provides users a Web accessible, platform independent interface to query, browse, and retrieve multimedia data such as images, graphics, audio, video from a large multimedia data repository. By integrating the multimedia DBMS, in which the textual information and samples of the multimedia data is organized and stored, and Web server together into the Microsoft ActiveX Server Framework, users can access the DBMS and query the information by simply using a Web browser at the client-side. The original multimedia data can then be located and transmitted through the Internet from the tertiary storage device, a 400 CDROM optical jukebox at the server-side, to the client-side for further use.

The THOSE remote interface

NASA Astrophysics Data System (ADS)

Klawon, Kevin; Gold, Josh; Bachman, Kristen

2013-05-01

The DIA, in conjunction with the Army Research Lab (ARL), wants to create an Unmanned Ground Sensor (UGS) controller that is (a) interoperable across all controller platforms, (b) capable of easily adding new sensors, radios, and processes and (c) backward compatible with existing UGS systems. To achieve this, a Terra Harvest controller was created that used Java JRE 1.6 and an Open Services Gateway initiative (OSGi) platform, named Terra Harvest Open Software Environment (THOSE). OSGi is an extensible framework that provides a modularized environment for deploying functionality in "bundles". These bundles can publish, discover, and share services available from other external bundles or bundles provided by the controller core. With the addition of a web GUI used for interacting with THOSE, a natural step was then to create a common remote interface that allows 3rd party real-time interaction with the controller. This paper provides an overview of the THOSE system and its components as well as a description of the architectural structure of the remote interface, highlighting the interactions occurring between the controller and the remote interface and its role in providing a positive user experience for managing UGSS functions.

Prototype and Evaluation of AutoHelp: A Case-based, Web-accessible Help Desk System for EOSDIS

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.; Thurman, David A.

1999-01-01

AutoHelp is a case-based, Web-accessible help desk for users of the EOSDIS. Its uses a combination of advanced computer and Web technologies, knowledge-based systems tools, and cognitive engineering to offload the current, person-intensive, help desk facilities at the DAACs. As a case-based system, AutoHelp starts with an organized database of previous help requests (questions and answers) indexed by a hierarchical category structure that facilitates recognition by persons seeking assistance. As an initial proof-of-concept demonstration, a month of email help requests to the Goddard DAAC were analyzed and partially organized into help request cases. These cases were then categorized to create a preliminary case indexing system, or category structure. This category structure allows potential users to identify or recognize categories of questions, responses, and sample cases similar to their needs. Year one of this research project focused on the development of a technology demonstration. User assistance 'cases' are stored in an Oracle database in a combination of tables linking prototypical questions with responses and detailed examples from the email help requests analyzed to date. When a potential user accesses the AutoHelp system, a Web server provides a Java applet that displays the category structure of the help case base organized by the needs of previous users. When the user identifies or requests a particular type of assistance, the applet uses Java database connectivity (JDBC) software to access the database and extract the relevant cases. The demonstration will include an on-line presentation of how AutoHelp is currently structured. We will show how a user might request assistance via the Web interface and how the AutoHelp case base provides assistance. The presentation will describe the DAAC data collection, case definition, and organization to date, as well as the AutoHelp architecture. It will conclude with the year 2 proposal to more fully develop the case base, the user interface (including the category structure), interface with the current DAAC Help System, the development of tools to add new cases, and user testing and evaluation at (perhaps) the Goddard DAAC.

Web-based volume slicer for 3D electron-microscopy data from EMDB

PubMed Central

Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J.; Patwardhan, Ardan

2016-01-01

We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale. PMID:26876163

Columbia University's Informatics for Diabetes Education and Telemedicine (IDEATel) Project

PubMed Central

Starren, Justin; Hripcsak, George; Sengupta, Soumitra; Abbruscato, C.R.; Knudson, Paul E.; Weinstock, Ruth S.; Shea, Steven

2002-01-01

The Columbia University Informatics for Diabetes Education and Telemedicine IDEATel) project is a four-year demonstration project funded by the Centers for Medicare and Medicaid Services with the overall goal of evaluating the feasibility, acceptability, effectiveness, and cost-effectiveness of telemedicine. The focal point of the intervention is the home telemedicine unit (HTU), which provides four functions: synchronous videoconferencing over standard telephone lines, electronic transmission for fingerstick glucose and blood pressure readings, secure Web-based messaging and clinical data review, and access to Web-based educational materials. The HTU must be usable by elderly patients with no prior computer experience. Providing these functions through the HTU requires tight integration of six components: the HTU itself, case management software, a clinical information system, Web-based educational material, data security, and networking and telecommunications. These six components were integrated through a variety of interfaces, providing a system that works well for patients and providers. With more than 400 HTUs installed, IDEATel has demonstrated the feasibility of large-scale home telemedicine. PMID:11751801

New Web Services for Broader Access to National Deep Submergence Facility Data Resources Through the Interdisciplinary Earth Data Alliance

NASA Astrophysics Data System (ADS)

Ferrini, V. L.; Grange, B.; Morton, J. J.; Soule, S. A.; Carbotte, S. M.; Lehnert, K.

2016-12-01

The National Deep Submergence Facility (NDSF) operates the Human Occupied Vehicle (HOV) Alvin, the Remotely Operated Vehicle (ROV) Jason, and the Autonomous Underwater Vehicle (AUV) Sentry. These vehicles are deployed throughout the global oceans to acquire sensor data and physical samples for a variety of interdisciplinary science programs. As part of the EarthCube Integrative Activity Alliance Testbed Project (ATP), new web services were developed to improve access to existing online NDSF data and metadata resources. These services make use of tools and infrastructure developed by the Interdisciplinary Earth Data Alliance (IEDA) and enable programmatic access to metadata and data resources as well as the development of new service-driven user interfaces. The Alvin Frame Grabber and Jason Virtual Van enable the exploration of frame-grabbed images derived from video cameras on NDSF dives. Metadata available for each image includes time and vehicle position, data from environmental sensors, and scientist-generated annotations, and data are organized and accessible by cruise and/or dive. A new FrameGrabber web service and service-driven user interface were deployed to offer integrated access to these data resources through a single API and allows users to search across content curated in both systems. In addition, a new NDSF Dive Metadata web service and service-driven user interface was deployed to provide consolidated access to basic information about each NDSF dive (e.g. vehicle name, dive ID, location, etc), which is important for linking distributed data resources curated in different data systems.

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

PubMed

Rowe, Will; Baker, Kate S; Verner-Jeffreys, David; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan; Pearce, Gareth

2015-01-01

Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.

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.

DDS as middleware of the Southern African Large Telescope control system

NASA Astrophysics Data System (ADS)

Maartens, Deneys S.; Brink, Janus D.

2016-07-01

The Southern African Large Telescope (SALT) software control system1 is realised as a distributed control system, implemented predominantly in National Instruments' LabVIEW. The telescope control subsystems communicate using cyclic, state-based messages. Currently, transmitting a message is accomplished by performing an HTTP PUT request to a WebDAV directory on a centralised Apache web server, while receiving is based on polling the web server for new messages. While the method works, it presents a number of drawbacks; a scalable distributed communication solution with minimal overhead is a better fit for control systems. This paper describes our exploration of the Data Distribution Service (DDS). DDS is a formal standard specification, defined by the Object Management Group (OMG), that presents a data-centric publish-subscribe model for distributed application communication and integration. It provides an infrastructure for platform- independent many-to-many communication. A number of vendors provide implementations of the DDS standard; RTI, in particular, provides a DDS toolkit for LabVIEW. This toolkit has been evaluated against the needs of SALT, and a few deficiencies have been identified. We have developed our own implementation that interfaces LabVIEW to DDS in order to address our specific needs. Our LabVIEW DDS interface implementation is built against the RTI DDS Core component, provided by RTI under their Open Community Source licence. Our needs dictate that the interface implementation be platform independent. Since we have access to the RTI DDS Core source code, we are able to build the RTI DDS libraries for any of the platforms on which we require support. The communications functionality is based on UDP multicasting. Multicasting is an efficient communications mechanism with low overheads which avoids duplicated point-to-point transmission of data on a network where there are multiple recipients of the data. In the paper we present a performance evaluation of DDS against the current HTTP-based implementation as well as the historical DataSocket implementation. We conclude with a summary and describe future work.

The Live Access Server - A Web-Services Framework for Earth Science Data

NASA Astrophysics Data System (ADS)

Schweitzer, R.; Hankin, S. C.; Callahan, J. S.; O'Brien, K.; Manke, A.; Wang, X. Y.

2005-12-01

The Live Access Server (LAS) is a general purpose Web-server for delivering services related to geo-science data sets. Data providers can use the LAS architecture to build custom Web interfaces to their scientific data. Users and client programs can then access the LAS site to search the provider's on-line data holdings, make plots of data, create sub-sets in a variety of formats, compare data sets and perform analysis on the data. The Live Access server software has continued to evolve by expanding the types of data (in-situ observations and curvilinear grids) it can serve and by taking advantages of advances in software infrastructure both in the earth sciences community (THREDDS, the GrADS Data Server, the Anagram framework and Java netCDF 2.2) and in the Web community (Java Servlet and the Apache Jakarta frameworks). This presentation will explore the continued evolution of the LAS architecture towards a complete Web-services-based framework. Additionally, we will discuss the redesign and modernization of some of the support tools available to LAS installers. Soon after the initial implementation, the LAS architecture was redesigned to separate the components that are responsible for the user interaction (the User Interface Server) from the components that are responsible for interacting with the data and producing the output requested by the user (the Product Server). During this redesign, we changed the implementation of the User Interface Server from CGI and JavaScript to the Java Servlet specification using Apache Jakarta Velocity backed by a database store for holding the user interface widget components. The User Interface server is now quite flexible and highly configurable because we modernized the components used for the implementation. Meanwhile, the implementation of the Product Server has remained a Perl CGI-based system. Clearly, the time has come to modernize this part of the LAS architecture. Before undertaking such a modernization it is important to understand what we hope to gain. Specifically we would like to make it even easier to add new output products into our core system based on the Ferret analysis and visualization package. By carefully factoring the tasks needed to create a product we will be able to create new products simply by adding a description of the product into the configuration and by writing the Ferret script needed to create the product. No code will need to be added to the Product Server to bring the new product on-line. The new architecture should be faster at extracting and processing configuration information needed to address each request. Finally, the new Product Server architecture should make it even easier to pass specialized configuration information to the Product Server to deal with unanticipated special data structures or processing requirements.

Does Interface Matter? A Study of Web Authoring and Editing by Inexperienced Web Writers

ERIC Educational Resources Information Center

Dick, Rodney F.

2006-01-01

This study explores the complicated nature of the interface as a mediational tool for inexperienced writers as they composed hypertext documents. Because technology can become so quickly and inextricably connected to people's everyday lives, it is essential to explore the effects on these technologies before they become invisible. Because…

Web-Based Interactive Electronic Technical Manual (IETM) Common User Interface Style Guide, Version 2.0

DTIC Science & Technology

2003-07-01

Technical Report WEB-BASED INTERACTIVE ELECTRONIC TECHNICAL MANUAL (IETM) COMMON USER INTERFACE STYLE GUIDE Version 2.0 – July 2003 by L. John Junod ...ACKNOWLEDGEMENTS The principal authors of this document were: John Junod – NSWC, Carderock Division, Phil Deuell – AMSEC LLC, Kathleen Moore

A novel web-enabled healthcare solution on health vault system.

PubMed

Liao, Lingxia; Chen, Min; Rodrigues, Joel J P C; Lai, Xiaorong; Vuong, Son

2012-06-01

Complicated Electronic Medical Records (EMR) systems have created problems in systems regarding an easy implementation and interoperability for a Web-enabled Healthcare Solution, which is normally provided by an independent healthcare giver with limited IT knowledge and interests. An EMR system with well-designed and user-friendly interface, such as Microsoft HealthVault System used as the back-end platform of a Web-enabled healthcare application will be an approach to deal with these problems. This paper analyzes the patient oriented Web-enabled healthcare service application as the new trend to delivery healthcare from hospital/clinic-centric to patient-centric, the current e-healthcare applications, and the main backend EMR systems. Then, we present a novel web-enabled healthcare solution based on Microsoft HealthVault EMR system to meet customers' needs, such as, low total cost, easily development and maintenance, and good interoperability. A sample system is given to show how the solution can be fulfilled, evaluated, and validated. We expect that this paper will provide a deep understanding of the available EMR systems, leading to insights for new solutions and approaches driven to next generation EMR systems.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

A reliable user authentication and key agreement scheme for Web-based Hospital-acquired Infection Surveillance Information System.

PubMed

Wu, Zhen-Yu; Tseng, Yi-Ju; Chung, Yufang; Chen, Yee-Chun; Lai, Feipei

2012-08-01

With the rapid development of the Internet, both digitization and electronic orientation are required on various applications in the daily life. For hospital-acquired infection control, a Web-based Hospital-acquired Infection Surveillance System was implemented. Clinical data from different hospitals and systems were collected and analyzed. The hospital-acquired infection screening rules in this system utilized this information to detect different patterns of defined hospital-acquired infection. Moreover, these data were integrated into the user interface of a signal entry point to assist physicians and healthcare providers in making decisions. Based on Service-Oriented Architecture, web-service techniques which were suitable for integrating heterogeneous platforms, protocols, and applications, were used. In summary, this system simplifies the workflow of hospital infection control and improves the healthcare quality. However, it is probable for attackers to intercept the process of data transmission or access to the user interface. To tackle the illegal access and to prevent the information from being stolen during transmission over the insecure Internet, a password-based user authentication scheme is proposed for information integrity.

"Just Another Tool for Online Studies” (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies

PubMed Central

Lange, Kristian; Kühn, Simone; Filevich, Elisa

2015-01-01

We present here “Just Another Tool for Online Studies” (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS’ main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org. PMID:26114751

Lightweight monitoring and control system for coal mine safety using REST style.

PubMed

Cheng, Bo; Cheng, Xin; Chen, Junliang

2015-01-01

The complex environment of a coal mine requires the underground environment, devices and miners to be constantly monitored to ensure safe coal production. However, existing coal mines do not meet these coverage requirements because blind spots occur when using a wired network. In this paper, we develop a Web-based, lightweight remote monitoring and control platform using a wireless sensor network (WSN) with the REST style to collect temperature, humidity and methane concentration data in a coal mine using sensor nodes. This platform also collects information on personnel positions inside the mine. We implement a RESTful application programming interface (API) that provides access to underground sensors and instruments through the Web such that underground coal mine physical devices can be easily interfaced to remote monitoring and control applications. We also implement three different scenarios for Web-based, lightweight remote monitoring and control of coal mine safety and measure and analyze the system performance. Finally, we present the conclusions from this study and discuss future work. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

Envisioning Advanced User Interfaces for E-Government Applications: A Case Study

NASA Astrophysics Data System (ADS)

Calvary, Gaëlle; Serna, Audrey; Coutaz, Joëlle; Scapin, Dominique; Pontico, Florence; Winckler, Marco

The increasing use of the Web as a software platform together with the advance of technology has promoted Web applications as a starting point for improving communication between citizens and administration. Currently, several e-government Web portals propose applications for accessing information regarding healthcare, taxation, registration, housing, agriculture, education, and social services, which otherwise may be difficult to obtain. However, the adoption of services provided to citizens depends upon how such applications comply with the users' needs. Unfortunately, building an e-government website doesn't guarantee that all citizens who come to use it can access its contents. These services need to be accessible to all citizens/customers equally to ensure wider reach and subsequent adoption of the e-government services. User disabilities, computer or language illiteracy (e.g., foreign language), flexibility on information access (e.g., user remotely located in rural areas, homeless, mobile users), and ensuring user privacy on sensitive data are some of the barriers that must be taken into account when designing the User Interface (UI) of e-government applications.

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

CFGP: a web-based, comparative fungal genomics platform

PubMed Central

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F.; Blair, Jaime E.; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the ‘fill-in-the-form-and-press-SUBMIT’ user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI. PMID:17947331

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

New Data Products and Tools from STEREO's IMPACT Investigation

NASA Astrophysics Data System (ADS)

Schroeder, P. C.; Luhmann, J. G.; Li, Y.; Huttunen, E.; Toy, V.; Russell, C. T.; Davis, A.

2008-05-01

STEREO's IMPACT (In-situ Measurements of Particles and CME Transients) investigation provides the first opportunity for long duration, detailed observations of 1 AU magnetic field structures, plasma and suprathermal electrons, and energetic particles at points bracketing Earth's heliospheric location. The IMPACT team has developed both human-friendly web portals and API's (application program interfaces) which provide straight- foward data access to scientists and the Virtual Observatories. Several new data products and web features have been developed including the release of more and higher-level data products, a library of TPLOT-based IDL data analysis routines, and web sites devoted to event analysis and inter-mission and inter-disciplinary collaboration. A web browser integrating STEREO and L1 in situ data with imaging and models provides a powerful venue for exploring the Sun-Earth connection. These latest releases enable the larger scientific community to use STEREO's unique in-situ data in novel ways along side "third eye" data sets from Wind, ACE and other heliospheric missions contributing to a better understanding of three dimensional structures in the solar wind.

Dietary Supplement Label Database (DSLD)

Science.gov Websites

Intakes (DRIs) Definitions Frequently Asked Questions (FAQ) Information Sources Release Notes Help Search full label derived information from dietary supplement products marketed in the U.S. with a Web-based user interface that provides ready access to label information. It was developed to serve the research

Information Portals: The Next Generation Catalog

ERIC Educational Resources Information Center

Allison, DeeAnn

2010-01-01

Libraries today face an increasing challenge: to provide relevant information to diverse populations with differing needs while competing with Web search engines like Google. In 2009, a large group of libraries, including the University of Nebraska-Lincoln Libraries, joined with Innovative Interfaces as development partners to design a new type of…

Building Geospatial Web Services for Ecological Monitoring and Forecasting

NASA Astrophysics Data System (ADS)

Hiatt, S. H.; Hashimoto, H.; Melton, F. S.; Michaelis, A. R.; Milesi, C.; Nemani, R. R.; Wang, W.

2008-12-01

The Terrestrial Observation and Prediction System (TOPS) at NASA Ames Research Center is a modeling system that generates a suite of gridded data products in near real-time that are designed to enhance management decisions related to floods, droughts, forest fires, human health, as well as crop, range, and forest production. While these data products introduce great possibilities for assisting management decisions and informing further research, realization of their full potential is complicated by their shear volume and by the need for a necessary infrastructure for remotely browsing, visualizing, and analyzing the data. In order to address these difficulties we have built an OGC-compliant WMS and WCS server based on an open source software stack that provides standardized access to our archive of data. This server is built using the open source Java library GeoTools which achieves efficient I/O and image rendering through Java Advanced Imaging. We developed spatio-temporal raster management capabilities using the PostGrid raster indexation engine. We provide visualization and browsing capabilities through a customized Ajax web interface derived from the kaMap project. This interface allows resource managers to quickly assess ecosystem conditions and identify significant trends and anomalies from within their web browser without the need to download source data or install special software. Our standardized web services also expose TOPS data to a range of potential clients, from web mapping applications to virtual globes and desktop GIS packages. However, support for managing the temporal dimension of our data is currently limited in existing software systems. Future work will attempt to overcome this shortcoming by building time-series visualization and analysis tools that can be integrated with existing geospatial software.

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.

PubMed

Zhang, Dong; Xue, Xingran; Malmberg, Russell L; Cai, Liming

2012-10-15

TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To date, there are five core sub-structures commonly found in TR of fungal species, which are the template region, downstream pseudoknot, boundary element, core-closing stem and triple helix. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species. The web server TRFolder-W is available at http://rna-informatics.uga.edu/?f=software&p=TRFolder-w.

Web Audio/Video Streaming Tool

NASA Technical Reports Server (NTRS)

Guruvadoo, Eranna K.

2003-01-01

In order to promote NASA-wide educational outreach program to educate and inform the public of space exploration, NASA, at Kennedy Space Center, is seeking efficient ways to add more contents to the web by streaming audio/video files. This project proposes a high level overview of a framework for the creation, management, and scheduling of audio/video assets over the web. To support short-term goals, the prototype of a web-based tool is designed and demonstrated to automate the process of streaming audio/video files. The tool provides web-enabled users interfaces to manage video assets, create publishable schedules of video assets for streaming, and schedule the streaming events. These operations are performed on user-defined and system-derived metadata of audio/video assets stored in a relational database while the assets reside on separate repository. The prototype tool is designed using ColdFusion 5.0.

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Chromothripsis Detection and Characterization Using the CTLPScanner Web Server.

PubMed

Yang, Jian; Liu, Bo; Cai, Haoyang

2018-01-01

Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner ( http://cgma.scu.edu.cn/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate the utility of CTLPScanner for screening chromosome pulverization regions and give interpretation of the results. The web interface offers a set of parameters and thresholds for customized screening. We also provide practical recommendations for effective chromothripsis detection. In addition to the user data processing module, CTLPScanner contains more than 50,000 preprocessed oncogenomic arrays, which allow users to explore the presence of chromothripsis signatures from public data resources.

The OGC Sensor Web Enablement framework

NASA Astrophysics Data System (ADS)

Cox, S. J.; Botts, M.

2006-12-01

Sensor observations are at the core of natural sciences. Improvements in data-sharing technologies offer the promise of much greater utilisation of observational data. A key to this is interoperable data standards. The Open Geospatial Consortium's (OGC) Sensor Web Enablement initiative (SWE) is developing open standards for web interfaces for the discovery, exchange and processing of sensor observations, and tasking of sensor systems. The goal is to support the construction of complex sensor applications through real-time composition of service chains from standard components. The framework is based around a suite of standard interfaces, and standard encodings for the message transferred between services. The SWE interfaces include: Sensor Observation Service (SOS)-parameterized observation requests (by observation time, feature of interest, property, sensor); Sensor Planning Service (SPS)-tasking a sensor- system to undertake future observations; Sensor Alert Service (SAS)-subscription to an alert, usually triggered by a sensor result exceeding some value. The interface design generally follows the pattern established in the OGC Web Map Service (WMS) and Web Feature Service (WFS) interfaces, where the interaction between a client and service follows a standard sequence of requests and responses. The first obtains a general description of the service capabilities, followed by obtaining detail required to formulate a data request, and finally a request for a data instance or stream. These may be implemented in a stateless "REST" idiom, or using conventional "web-services" (SOAP) messaging. In a deployed system, the SWE interfaces are supplemented by Catalogue, data (WFS) and portrayal (WMS) services, as well as authentication and rights management. The standard SWE data formats are Observations and Measurements (O&M) which encodes observation metadata and results, Sensor Model Language (SensorML) which describes sensor-systems, Transducer Model Language (TML) which covers low-level data streams, and domain-specific GML Application Schemas for definitions of the target feature types. The SWE framework has been demonstrated in several interoperability testbeds. These were based around emergency management, security, contamination and environmental monitoring scenarios.

Climate Model Diagnostic Analyzer Web Service System

NASA Astrophysics Data System (ADS)

Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Jiang, J. H.

2014-12-01

We have developed a cloud-enabled web-service system that empowers physics-based, multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks. The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the observational datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation, (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs, and (3) ECMWF reanalysis outputs for several environmental variables in order to supplement observational datasets. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, (4) the calculation of difference between two variables, and (5) the conditional sampling of one physical variable with respect to another variable. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA will be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. In order to support 30+ simultaneous users during the school, we have deployed CMDA to the Amazon cloud environment. The cloud-enabled CMDA will provide each student with a virtual machine while the user interaction with the system will remain the same through web-browser interfaces. The summer school will serve as a valuable testbed for the tool development, preparing CMDA to serve its target community: Earth-science modeling and model-analysis community.

Sally Ride EarthKAM - Automated Image Geo-Referencing Using Google Earth Web Plug-In

NASA Technical Reports Server (NTRS)

Andres, Paul M.; Lazar, Dennis K.; Thames, Robert Q.

2013-01-01

Sally Ride EarthKAM is an educational program funded by NASA that aims to provide the public the ability to picture Earth from the perspective of the International Space Station (ISS). A computer-controlled camera is mounted on the ISS in a nadir-pointing window; however, timing limitations in the system cause inaccurate positional metadata. Manually correcting images within an orbit allows the positional metadata to be improved using mathematical regressions. The manual correction process is time-consuming and thus, unfeasible for a large number of images. The standard Google Earth program allows for the importing of KML (keyhole markup language) files that previously were created. These KML file-based overlays could then be manually manipulated as image overlays, saved, and then uploaded to the project server where they are parsed and the metadata in the database is updated. The new interface eliminates the need to save, download, open, re-save, and upload the KML files. Everything is processed on the Web, and all manipulations go directly into the database. Administrators also have the control to discard any single correction that was made and validate a correction. This program streamlines a process that previously required several critical steps and was probably too complex for the average user to complete successfully. The new process is theoretically simple enough for members of the public to make use of and contribute to the success of the Sally Ride EarthKAM project. Using the Google Earth Web plug-in, EarthKAM images, and associated metadata, this software allows users to interactively manipulate an EarthKAM image overlay, and update and improve the associated metadata. The Web interface uses the Google Earth JavaScript API along with PHP-PostgreSQL to present the user the same interface capabilities without leaving the Web. The simpler graphical user interface will allow the public to participate directly and meaningfully with EarthKAM. The use of similar techniques is being investigated to place ground-based observations in a Google Mars environment, allowing the MSL (Mars Science Laboratory) Science Team a means to visualize the rover and its environment.

The Index to Marine and Lacustrine Geological Samples (IMLGS): Linking Digital Data to Physical Samples for the Marine Community

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Jencks, J. H.; Eakins, B.

2016-12-01

The Index to Marine and Lacustrine Geological Samples (IMLGS) is a community designed and maintained resource enabling researchers to locate and request seafloor and lakebed geologic samples curated by partner institutions. The Index was conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center, now the National Centers for Environmental Information (NCEI), at a 1977 meeting convened by the National Science Foundation (NSF). The Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. The Curators Consortium, international in scope, meets biennially to share ideas and discuss best practices. NCEI serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the laborious task of creating and contributing metadata for over 205,000 sea floor and lake-bed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The IMLGS has a persistent URL/Digital Object Identifier (DOI), as well as DOIs assigned to partner collections for citation and to provide a persistent link to curator collections. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images : 1) at participating institutions, 2) in the NCEI archive, and 3) through a Linked Data interface maintained by the Rolling Deck to Repository R2R. Over 43,000 International GeoSample Numbers (IGSNs) linking to the System for Earth Sample Registration (SESAR) are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. The paper will discuss the database with a goal to increase the connections and links to related data at partner institutions.

Real-time shipboard displays for science operation and planning on CGC Healy

NASA Astrophysics Data System (ADS)

Roberts, S.; Chayes, D.; Arko, R.

2007-12-01

To facilitate effective science planning and decision making, we have developed a real-time geospatial browser and other displays widely used by many if not all members of USCGC Healy's science cruises and some officers and crew since 2004. In order to enable a 'zero-configuration' experience to the end user with nearly any modern browser, on any platform, anywhere on the ship with wired (or wireless) network access, we chose a Web-based/server-centric approach that provides a very low barrier to access in an environment where we have many participants constantly coming and going, often with their own computers. The principle interface for planning and operational decision making is a georeferenced, Web-based user interface built on the MapServer Web GIS platform developed at the University of Minnesota (http://mapserver.gis.umn.edu/), using the PostGIS spatial database extensions (http://postgis.refractions.net/) to enable live database connectivity. Data available include current ship position and orientation, historical ship tracks and data, seafloor bathymetry, station locations, RADARSAT, and subbottom profiles among others. In addition to the user interfaces that are part of individual instrumentation (such as the sonars and navigation systems), custom interfaces have been developed to centralize data with high update rates such as sea surface temperature, vessel attitude, position, etc. Underlying data acquisition and storage is provided by the Lamont Data System (LDS) and the NOAA SCS system. All data are stored on RAIDed disk systems and shared across a switched network with a gigabit fiber backbone. The real-time displays access data in a number of ways including real-time UDP datagrams from LDS, accessing files on disk, and querying a PostgreSQL relational backend. This work is supported by grants from the U.S. National Science Foundation, Office of Polar Programs, Arctic Science section.

BioFET-SIM web interface: implementation and two applications.

PubMed

Hediger, Martin R; Jensen, Jan H; De Vico, Luca

2012-01-01

We present a web interface which allows us to conveniently set up calculations based on the BioFET-SIM model. With the interface, the signal of a BioFET sensor can be calculated depending on its parameters, as well as the signal dependence on pH. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

NABIC marker database: A molecular markers information network of agricultural crops.

PubMed

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Remote health monitoring using mobile phones and Web services.

PubMed

Agarwal, Sparsh; Lau, Chiew Tong

2010-06-01

Diabetes and hypertension have become very common perhaps because of increasingly busy lifestyles, unhealthy eating habits, and a highly competitive workplace. The rapid advancement of mobile communication technologies offers innumerable opportunities for the development of software and hardware applications for remote monitoring of such chronic diseases. This study describes a remote health-monitoring service that provides an end-to-end solution, that is, (1) it collects blood pressure readings from the patient through a mobile phone; (2) it provides these data to doctors through a Web interface; and (3) it enables doctors to manage the chronic condition by providing feedback to the patients remotely. This article also aims at understanding the requirements and expectations of doctors and hospitals from such a remote health-monitoring service.

User Driven Image Stacking for ODI Data and Beyond via a Highly Customizable Web Interface

NASA Astrophysics Data System (ADS)

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

2015-09-01

While some astronomical archives have begun serving standard calibrated data products, the process of producing stacked images remains a challenge left to the end-user. The benefits of astronomical image stacking are well established, and dither patterns are recommended for almost all observing targets. Some archives automatically produce stacks of limited scientific usefulness without any fine-grained user or operator configurability. In this paper, we present PPA Stack, a web based stacking framework within the ODI - Portal, Pipeline, and Archive system. PPA Stack offers a web user interface with built-in heuristics (based on pointing, filter, and other metadata information) to pre-sort images into a set of likely stacks while still allowing the user or operator complete control over the images and parameters for each of the stacks they wish to produce. The user interface, designed using AngularJS, provides multiple views of the input dataset and parameters, all of which are synchronized in real time. A backend consisting of a Python application optimized for ODI data, wrapped around the SWarp software, handles the execution of stacking workflow jobs on Indiana University's Big Red II supercomputer, and the subsequent ingestion of the combined images back into the PPA archive. PPA Stack is designed to enable seamless integration of other stacking applications in the future, so users can select the most appropriate option for their science.

Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

PubMed Central

2013-01-01

Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents. Results In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it. PMID:23734622

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

PubMed Central

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

2010-01-01

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

The Joy of Playing with Oceanographic Data

NASA Astrophysics Data System (ADS)

Smith, A. T.; Xing, Z.; Armstrong, E. M.; Thompson, C. K.; Huang, T.

2013-12-01

The web is no longer just an after thought. It is no longer just a presentation layer filled with HTML, CSS, JavaScript, Frameworks, 3D, and more. It has become the medium of our communication. It is the database of all databases. It is the computing platform of all platforms. It has transformed the way we do science. Web service is the de facto method for communication between machines over the web. Representational State Transfer (REST) has standardized the way we architect services and their interfaces. In the Earth Science domain, we are familiar with tools and services such as Open-Source Project for Network Data Access Protocol (OPeNDAP), Thematic Realtime Environmental Distributed Data Services (THREDDS), and Live Access Server (LAS). We are also familiar with various data formats such as NetCDF3/4, HDF4/5, GRIB, TIFF, etc. One of the challenges for the Earth Science community is accessing information within these data. There are community-accepted readers that our users can download and install. However, the Application Programming Interface (API) between these readers is not standardized, which leads to non-portable applications. Webification (w10n) is an emerging technology, developed at the Jet Propulsion Laboratory, which exploits the hierarchical nature of a science data artifact to assign a URL to each element within the artifact. (e.g. a granule file). By embracing standards such as JSON, XML, and HTML5 and predictable URL, w10n provides a simple interface that enables tool-builders and researchers to develop portable tools/applications to interact with artifacts of various formats. The NASA Physical Oceanographic Distributed Active Archive Center (PO.DAAC) is the designated data center for observational products relevant to the physical state of the ocean. Over the past year PO.DAAC has been evaluating w10n technology by webifying its archive holdings to provide simplified access to oceanographic science artifacts and as a service to enable future tools and services development. In this talk, we will focus on a w10n-based system called Distributed Oceanographic Webification Service (DOWS) being developed at PO.DAAC to provide a newer and simpler method for working with observational data artifacts. As a continued effort at PO.DAAC to provide better tools and services to visualize our data, the talk will discuss the latest in web-based data visualization tools/frameworks (such as d3.js, Three.js, Leaflet.js, and more) and techniques for working with webified oceanographic science data in both a 2D and 3D web approach.

An intelligent tool for activity data collection.

PubMed

Sarkar, A M Jehad

2011-01-01

Activity recognition systems using simple and ubiquitous sensors require a large variety of real-world sensor data for not only evaluating their performance but also training the systems for better functioning. However, a tremendous amount of effort is required to setup an environment for collecting such data. For example, expertise and resources are needed to design and install the sensors, controllers, network components, and middleware just to perform basic data collections. It is therefore desirable to have a data collection method that is inexpensive, flexible, user-friendly, and capable of providing large and diverse activity datasets. In this paper, we propose an intelligent activity data collection tool which has the ability to provide such datasets inexpensively without physically deploying the testbeds. It can be used as an inexpensive and alternative technique to collect human activity data. The tool provides a set of web interfaces to create a web-based activity data collection environment. It also provides a web-based experience sampling tool to take the user's activity input. The tool generates an activity log using its activity knowledge and the user-given inputs. The activity knowledge is mined from the web. We have performed two experiments to validate the tool's performance in producing reliable datasets.

caCORE: a common infrastructure for cancer informatics.

PubMed

Covitz, Peter A; Hartel, Frank; Schaefer, Carl; De Coronado, Sherri; Fragoso, Gilberto; Sahni, Himanso; Gustafson, Scott; Buetow, Kenneth H

2003-12-12

Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).

Application of crowdsourced hail data and damage information for hail risk assessment in the province of Styria, Austria

NASA Astrophysics Data System (ADS)

Tani, Satyanarayana; Rechberger, Andreas; Süsser Rechberger, Barbara; Teschl, Reinhard; Paulitsch, Helmut

2017-04-01

Hail storm damage is a major concern to the farmers in the province of Styria, Austria. Each year severe hail storms are causing damages to crops, resulting in losses of millions of euros. High spatial and timely ground truth information of the hail event and crop damage measurements are essential for better hail risk assessment. Usually, hail pad networks and visual damage surveys are used to collect the hail data and corresponding damage information. However, these hail pad networks are expensive and need laborious maintenance. The traditional crop damage assessment approaches are very labour-intensive and time-consuming. The advancements in information and communication technology (ICT) and the power of citizen based crowdsourcing data, will help to overcome these problems and ultimately provide a platform for data collection. A user-friendly and bilingual web interface was developed to collect hail data and crop damage information in the province of Styria, Austria. The dynamic web interface was developed using HTML5, JavaScript, and PHP7 combined with a MySQL database back-end. OpenStreetMap was integrated into the web interface and tile server optimised for an easy identification of geolocation information. The user needs an internet connection to transfer the data through smartphone or computer. Crowdsourced data will be quality tested and evaluated with 3D single polarisation C-band weather radar data to remove potential false reports. Further, the relationship between the reported hail events and radar-based hail detection algorithms (Waldvogel and Auer) and derived hail signature information intended for crop hail risk assessment will be investigated. The details about the web interface tool, application and verification methods to collect, analyse, and integrate different data sets are given. Further, the high spatial risk assessment information is communicated to support risk management policy.

The Effects of Metaphorical Interface on Germane Cognitive Load in Web-Based Instruction

ERIC Educational Resources Information Center

Cheon, Jongpil; Grant, Michael M.

2012-01-01

The purpose of this study was to examine the effects of a metaphorical interface on germane cognitive load in Web-based instruction. Based on cognitive load theory, germane cognitive load is a cognitive investment for schema construction and automation. A new instrument developed in a previous study was used to measure students' mental activities…

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)

Development of a medical module for disaster information systems.

PubMed

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

2014-01-01

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

Developing web-based data analysis tools for precision farming using R and Shiny

NASA Astrophysics Data System (ADS)

Jahanshiri, Ebrahim; Mohd Shariff, Abdul Rashid

2014-06-01

Technologies that are set to increase the productivity of agricultural practices require more and more data. Nevertheless, farming data is also being increasingly cheap to collect and maintain. Bulk of data that are collected by the sensors and samples need to be analysed in an efficient and transparent manner. Web technologies have long being used to develop applications that can assist the farmers and managers. However until recently, analysing the data in an online environment has not been an easy task especially in the eyes of data analysts. This barrier is now overcome by the availability of new application programming interfaces that can provide real-time web based data analysis. In this paper developing a prototype web based application for data analysis using new facilities in R statistical package and its web development facility, Shiny is explored. The pros and cons of this type of data analysis environment for precision farming are enumerated and future directions in web application development for agricultural data are discussed.

Mfold web server for nucleic acid folding and hybridization prediction

PubMed Central

Zuker, Michael

2003-01-01

The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’. PMID:12824337

ESAP plus: a web-based server for EST-SSR marker development.

PubMed

Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

2016-12-22

Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ .

Architecture of the local spatial data infrastructure for regional climate change research

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny

2013-04-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, etc.) are actively used in modeling and analysis of climate change for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset studies in the area of climate and environmental change require a special software support based on SDI approach. A dedicated architecture of the local spatial data infrastructure aiming at regional climate change analysis using modern web mapping technologies is presented. Geoportal is a key element of any SDI, allowing searching of geoinformation resources (datasets and services) using metadata catalogs, producing geospatial data selections by their parameters (data access functionality) as well as managing services and applications of cartographical visualization. It should be noted that due to objective reasons such as big dataset volume, complexity of data models used, syntactic and semantic differences of various datasets, the development of environmental geodata access, processing and visualization services turns out to be quite a complex task. Those circumstances were taken into account while developing architecture of the local spatial data infrastructure as a universal framework providing geodata services. So that, the architecture presented includes: 1. Effective in terms of search, access, retrieval and subsequent statistical processing, model of storing big sets of regional georeferenced data, allowing in particular to store frequently used values (like monthly and annual climate change indices, etc.), thus providing different temporal views of the datasets 2. General architecture of the corresponding software components handling geospatial datasets within the storage model 3. Metadata catalog describing in detail using ISO 19115 and CF-convention standards datasets used in climate researches as a basic element of the spatial data infrastructure as well as its publication according to OGC CSW (Catalog Service Web) specification 4. Computational and mapping web services to work with geospatial datasets based on OWS (OGC Web Services) standards: WMS, WFS, WPS 5. Geoportal as a key element of thematic regional spatial data infrastructure providing also software framework for dedicated web applications development To realize web mapping services Geoserver software is used since it provides natural WPS implementation as a separate software module. To provide geospatial metadata services GeoNetwork Opensource (http://geonetwork-opensource.org) product is planned to be used for it supports ISO 19115/ISO 19119/ISO 19139 metadata standards as well as ISO CSW 2.0 profile for both client and server. To implement thematic applications based on geospatial web services within the framework of local SDI geoportal the following open source software have been selected: 1. OpenLayers JavaScript library, providing basic web mapping functionality for the thin client such as web browser 2. GeoExt/ExtJS JavaScript libraries for building client-side web applications working with geodata services. The web interface developed will be similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. The work is partially supported by RF Ministry of Education and Science grant 8345, SB RAS Program VIII.80.2.1 and IP 131.

Research and development of web oriented remote sensing image publication system based on Servlet technique

NASA Astrophysics Data System (ADS)

Juanle, Wang; Shuang, Li; Yunqiang, Zhu

2005-10-01

According to the requirements of China National Scientific Data Sharing Program (NSDSP), the research and development of web oriented RS Image Publication System (RSIPS) is based on Java Servlet technique. The designing of RSIPS framework is composed of 3 tiers, which is Presentation Tier, Application Service Tier and Data Resource Tier. Presentation Tier provides user interface for data query, review and download. For the convenience of users, visual spatial query interface is included. Served as a middle tier, Application Service Tier controls all actions between users and databases. Data Resources Tier stores RS images in file and relationship databases. RSIPS is developed with cross platform programming based on Java Servlet tools, which is one of advanced techniques in J2EE architecture. RSIPS's prototype has been developed and applied in the geosciences clearinghouse practice which is among the experiment units of NSDSP in China.

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

PubMed Central

Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

2017-01-01

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. PMID:27789697

CADB: Conformation Angles DataBase of proteins

PubMed Central

Sheik, S. S.; Ananthalakshmi, P.; Bhargavi, G. Ramya; Sekar, K.

2003-01-01

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/. PMID:12520049

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

PubMed Central

Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

2008-01-01

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

Monitoring activities of satellite data processing services in real-time with SDDS Live Monitor

NASA Astrophysics Data System (ADS)

Duc Nguyen, Minh

2017-10-01

This work describes Live Monitor, the monitoring subsystem of SDDS - an automated system for space experiment data processing, storage, and distribution created at SINP MSU. Live Monitor allows operators and developers of satellite data centers to identify errors occurred in data processing quickly and to prevent further consequences caused by the errors. All activities of the whole data processing cycle are illustrated via a web interface in real-time. Notification messages are delivered to responsible people via emails and Telegram messenger service. The flexible monitoring mechanism implemented in Live Monitor allows us to dynamically change and control events being shown on the web interface on our demands. Physicists, whose space weather analysis models are functioning upon satellite data provided by SDDS, can use the developed RESTful API to monitor their own events and deliver customized notification messages by their needs.

Smart mobility solution with multiple input Output interface.

PubMed

Sethi, Aartika; Deb, Sujay; Ranjan, Prabhat; Sardar, Arghya

2017-07-01

Smart wheelchairs are commonly used to provide solution for mobility impairment. However their usage is limited primarily due to high cost owing from sensors required for giving input, lack of adaptability for different categories of input and limited functionality. In this paper we propose a smart mobility solution using smartphone with inbuilt sensors (accelerometer, camera and speaker) as an input interface. An Emotiv EPOC+ is also used for motor imagery based input control synced with facial expressions in cases of extreme disability. Apart from traction, additional functions like home security and automation are provided using Internet of Things (IoT) and web interfaces. Although preliminary, our results suggest that this system can be used as an integrated and efficient solution for people suffering from mobility impairment. The results also indicate a decent accuracy is obtained for the overall system.

Global Agricultural Monitoring (GLAM) using MODAPS and LANCE Data Products

NASA Astrophysics Data System (ADS)

Anyamba, A.; Pak, E. E.; Majedi, A. H.; Small, J. L.; Tucker, C. J.; Reynolds, C. A.; Pinzon, J. E.; Smith, M. M.

2012-12-01

The Global Inventory Modeling and Mapping Studies / Global Agricultural Monitoring (GIMMS GLAM) system is a web-based geographic application that offers Moderate Resolution Imaging Spectroradiometer (MODIS) imagery and user interface tools to data query and plot MODIS NDVI time series. The system processes near real-time and science quality Terra and Aqua MODIS 8-day composited datasets. These datasets are derived from the MOD09 and MYD09 surface reflectance products which are generated and provided by NASA/GSFC Land and Atmosphere Near Real-time Capability for EOS (LANCE) and NASA/GSFC MODIS Adaptive Processing System (MODAPS). The GIMMS GLAM system is developed and provided by the NASA/GSFC GIMMS group for the U.S. Department of Agriculture / Foreign Agricultural Service / International Production Assessment Division (USDA/FAS/IPAD) Global Agricultural Monitoring project (GLAM). The USDA/FAS/IPAD mission is to provide objective, timely, and regular assessment of the global agricultural production outlook and conditions affecting global food security. This system was developed to improve USDA/FAS/IPAD capabilities for making operational quantitative estimates for crop production and yield estimates based on satellite-derived data. The GIMMS GLAM system offers 1) web map imagery including Terra & Aqua MODIS 8-day composited NDVI, NDVI percent anomaly, and SWIR-NIR-Red band combinations, 2) web map overlays including administrative and 0.25 degree Land Information System (LIS) shape boundaries, and crop land cover masks, and 3) user interface tools to select features, data query, plot, and download MODIS NDVI time series.

Sharing knowledge of Planetary Datasets through the Web-Based PRoGIS

NASA Astrophysics Data System (ADS)

Giordano, M. G.; Morley, J. M.; Muller, J. P. M.; Barnes, R. B.; Tao, Y. T.

2015-10-01

The large amount of raw and derived data available from various planetary surface missions (e.g. Mars and Moon in our case) has been integrated withco-registered and geocoded orbital image data to provide rover traverses and camera site locations in universal global co-ordinates [1]. This then allows an integrated GIS to use these geocoded products for scientific applications: we aim to create a web interface, PRoGIS, with minimal controls focusing on the usability and visualisation of the data, to allow planetary geologists to share annotated surface observations. These observations in a common context are shared between different tools and software (PRoGIS, Pro3D, 3D point cloud viewer). Our aim is to use only Open Source components that integrate Open Web Services for planetary data to make available an universal platform with a WebGIS interface, as well as a 3D point cloud and a Panorama viewer to explore derived data. On top of these tools we are building capabilities to make and share annotations amongst users. We use Python and Django for the server-side framework and Open Layers 3 for the WebGIS client. For good performance previewing 3D data (point clouds, pictures on the surface and panoramas) we employ ThreeJS, a WebGL Javascript library. Additionally, user and group controls allow scientists to store and share their observations. PRoGIS not only displays data but also launches sophisticated 3D vision reprocessing (PRoVIP) and an immersive 3D analysis environment (PRo3D).

WebViz: A web browser based application for collaborative analysis of 3D data

NASA Astrophysics Data System (ADS)

Ruegg, C. S.

2011-12-01

In the age of high speed Internet where people can interact instantly, scientific tools have lacked technology which can incorporate this concept of communication using the web. To solve this issue a web application for geological studies has been created, tentatively titled WebViz. This web application utilizes tools provided by Google Web Toolkit to create an AJAX web application capable of features found in non web based software. Using these tools, a web application can be created to act as piece of software from anywhere in the globe with a reasonably speedy Internet connection. An application of this technology can be seen with data regarding the recent tsunami from the major japan earthquakes. After constructing the appropriate data to fit a computer render software called HVR, WebViz can request images of the tsunami data and display it to anyone who has access to the application. This convenience alone makes WebViz a viable solution, but the option to interact with this data with others around the world causes WebViz to be taken as a serious computational tool. WebViz also can be used on any javascript enabled browser such as those found on modern tablets and smart phones over a fast wireless connection. Due to the fact that WebViz's current state is built using Google Web Toolkit the portability of the application is in it's most efficient form. Though many developers have been involved with the project, each person has contributed to increase the usability and speed of the application. In the project's most recent form a dramatic speed increase has been designed as well as a more efficient user interface. The speed increase has been informally noticed in recent uses of the application in China and Australia with the hosting server being located at the University of Minnesota. The user interface has been improved to not only look better but the functionality has been improved. Major functions of the application are rotating the 3D object using buttons. These buttons have been replaced with a new layout that is easier to understand the function and is also easy to use with mobile devices. With these new changes, WebViz is easier to control and use for general use.

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

2017-11-01

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for online validation of Monte Carlo event samples through a web interface.

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

UnCover on the Web: search hints and applications in library environments.

PubMed

Galpern, N F; Albert, K M

1997-01-01

Among the huge maze of resources available on the Internet, UnCoverWeb stands out as a valuable tool for medical libraries. This up-to-date, free-access, multidisciplinary database of periodical references is searched through an easy-to-learn graphical user interface that is a welcome improvement over the telnet version. This article reviews the basic and advanced search techniques for UnCoverWeb, as well as providing information on the document delivery functions and table of contents alerting service called Reveal. UnCover's currency is evaluated and compared with other current awareness resources. System deficiencies are discussed, with the conclusion that although UnCoverWeb lacks the sophisticated features of many commercial database search services, it is nonetheless a useful addition to the repertoire of information sources available in a library.

Use of StreamStats in the Upper French Broad River Basin, North Carolina: A Pilot Water-Resources Web Application

USGS Publications Warehouse

Wagner, Chad R.; Tighe, Kirsten C.; Terziotti, Silvia

2009-01-01

StreamStats is a Web-based Geographic Information System (GIS) application that was developed by the U.S. Geological Survey (USGS) in cooperation with Environmental Systems Research Institute, Inc. (ESRI) to provide access to an assortment of analytical tools that are useful for water-resources planning and management. StreamStats allows users to easily obtain streamflow statistics, basin characteristics, and descriptive information for USGS data-collection sites and selected ungaged sites. StreamStats also allows users to identify stream reaches upstream and downstream from user-selected sites and obtain information for locations along streams where activities occur that can affect streamflow conditions. This functionality can be accessed through a map-based interface with the user's Web browser or through individual functions requested remotely through other Web applications.

A semantic web framework to integrate cancer omics data with biological knowledge.

PubMed

Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

2012-01-25

The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

PubMed Central

2010-01-01

Background There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. Methods The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. Results In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure. Conclusions The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org. PMID:21210979

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

DOE PAGES

Zerkin, V. V.; Pritychenko, B.

2018-02-04

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

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

NASA Astrophysics Data System (ADS)

Zerkin, V. V.; Pritychenko, B.

2018-04-01

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

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

PubMed Central

Xayaphoummine, A.; Bucher, T.; Isambert, H.

2005-01-01

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at . PMID:15980546

Jflow: a workflow management system for web applications.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Bardou, Philippe; Nabihoudine, Ibouniyamine; Noirot, Céline; Trotard, Marie-Stéphane; Gaspin, Christine; Klopp, Christophe

2016-02-01

Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows. Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal. Jerome.Mariette@toulouse.inra.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A grid-enabled web service for low-resolution crystal structure refinement.

PubMed

O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

2012-03-01

Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

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

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

Zerkin, V. V.; Pritychenko, B.

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

KAGLVis - On-line 3D Visualisation of Earth-observing-satellite Data

NASA Astrophysics Data System (ADS)

Szuba, Marek; Ameri, Parinaz; Grabowski, Udo; Maatouki, Ahmad; Meyer, Jörg

2015-04-01

One of the goals of the Large-Scale Data Management and Analysis project is to provide a high-performance framework facilitating management of data acquired by Earth-observing satellites such as Envisat. On the client-facing facet of this framework, we strive to provide visualisation and basic analysis tool which could be used by scientists with minimal to no knowledge of the underlying infrastructure. Our tool, KAGLVis, is a JavaScript client-server Web application which leverages modern Web technologies to provide three-dimensional visualisation of satellite observables on a wide range of client systems. It takes advantage of the WebGL API to employ locally available GPU power for 3D rendering; this approach has been demonstrated to perform well even on relatively weak hardware such as integrated graphics chipsets found in modern laptop computers and with some user-interface tuning could even be usable on embedded devices such as smartphones or tablets. Data is fetched from the database back-end using a ReST API and cached locally, both in memory and using HTML5 Web Storage, to minimise network use. Computations, calculation of cloud altitude from cloud-index measurements for instance, can depending on configuration be performed on either the client or the server side. Keywords: satellite data, Envisat, visualisation, 3D graphics, Web application, WebGL, MEAN stack.

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.

Remote Instrumentation for Teaching Laboratory

ERIC Educational Resources Information Center

Baran, Jit; Currie, Ron; Kennepohl, Dietmar

2004-01-01

The feasibility of using current software, such as PC-Duo, PCAnywhere or LabVIEW, in training students in instrumental analysis from a remote location is investigated. Findings show that creation of online features is crucial to the use and learning by students and the development of a suitable Web site, which provides an easy-to-use interface to…

Enabling On-Demand Database Computing with MIT SuperCloud Database Management System

DTIC Science & Technology

2015-09-15

arc.liv.ac.uk/trac/SGE) provides these services and is independent of programming language (C, Fortran, Java , Matlab, etc) or parallel programming...a MySQL database to store DNS records. The DNS records are controlled via a simple web service interface that allows records to be created

Spaces of the Hilltop: A Case Study of Community/Academic Interaction

ERIC Educational Resources Information Center

Knochel, Aaron; Selfe, Dickie

2012-01-01

The mapping imagery of the web interface is an attempt to illustrate the surprising element of the Hilltop project. The map is not "accurate." It shows real streets and highways in, around, and in-between the Ohio State University and the Hilltop community, but it is not intended to provide directions.

A Framework for Adaptive Learning Design in a Web-Conferencing Environment

ERIC Educational Resources Information Center

Bower, Matt

2016-01-01

Many recent technologies provide the ability to dynamically adjust the interface depending on the emerging cognitive and collaborative needs of the learning episode. This means that educators can adaptively re-design the learning environment during the lesson, rather than purely relying on preemptive learning design thinking. Based on a…

The online Tabloid Proteome: an annotated database of protein associations

PubMed Central

Turan, Demet; Tavernier, Jan

2018-01-01

Abstract A complete knowledge of the proteome can only be attained by determining the associations between proteins, along with the nature of these associations (e.g. physical contact in protein–protein interactions, participation in complex formation or different roles in the same pathway). Despite extensive efforts in elucidating direct protein interactions, our knowledge on the complete spectrum of protein associations remains limited. We therefore developed a new approach that detects protein associations from identifications obtained after re-processing of large-scale, public mass spectrometry-based proteomics data. Our approach infers protein association based on the co-occurrence of proteins across many different proteomics experiments, and provides information that is almost completely complementary to traditional direct protein interaction studies. We here present a web interface to query and explore the associations derived from this method, called the online Tabloid Proteome. The online Tabloid Proteome also integrates biological knowledge from several existing resources to annotate our derived protein associations. The online Tabloid Proteome is freely available through a user-friendly web interface, which provides intuitive navigation and data exploration options for the user at http://iomics.ugent.be/tabloidproteome. PMID:29040688

A user-friendly mathematical modelling web interface to assist local decision making in the fight against drug-resistant tuberculosis.

PubMed

Ragonnet, Romain; Trauer, James M; Denholm, Justin T; Marais, Ben J; McBryde, Emma S

2017-05-30

Multidrug-resistant and rifampicin-resistant tuberculosis (MDR/RR-TB) represent an important challenge for global tuberculosis (TB) control. The high rates of MDR/RR-TB observed among re-treatment cases can arise from diverse pathways: de novo amplification during initial treatment, inappropriate treatment of undiagnosed MDR/RR-TB, relapse despite appropriate treatment, or reinfection with MDR/RR-TB. Mathematical modelling allows quantification of the contribution made by these pathways in different settings. This information provides valuable insights for TB policy-makers, allowing better contextualised solutions. However, mathematical modelling outputs need to consider local data and be easily accessible to decision makers in order to improve their usefulness. We present a user-friendly web-based modelling interface, which can be used by people without technical knowledge. Users can input their own parameter values and produce estimates for their specific setting. This innovative tool provides easy access to mathematical modelling outputs that are highly relevant to national TB control programs. In future, the same approach could be applied to a variety of modelling applications, enhancing local decision making.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

High-performance web viewer for cardiac images

NASA Astrophysics Data System (ADS)

dos Santos, Marcelo; Furuie, Sergio S.

2004-04-01

With the advent of the digital devices for medical diagnosis the use of the regular films in radiology has decreased. Thus, the management and handling of medical images in digital format has become an important and critical task. In Cardiology, for example, the main difficulty is to display dynamic images with the appropriated color palette and frame rate used on acquisition process by Cath, Angio and Echo systems. In addition, other difficulty is handling large images in memory by any existing personal computer, including thin clients. In this work we present a web-based application that carries out these tasks with robustness and excellent performance, without burdening the server and network. This application provides near-diagnostic quality display of cardiac images stored as DICOM 3.0 files via a web browser and provides a set of resources that allows the viewing of still and dynamic images. It can access image files from the local disks, or network connection. Its features include: allows real-time playback, dynamic thumbnails image viewing during loading, access to patient database information, image processing tools, linear and angular measurements, on-screen annotations, image printing and exporting DICOM images to other image formats, and many others, all characterized by a pleasant user-friendly interface, inside a Web browser by means of a Java application. This approach offers some advantages over the most of medical images viewers, such as: facility of installation, integration with other systems by means of public and standardized interfaces, platform independence, efficient manipulation and display of medical images, all with high performance.

Design and development of a web-based application for diabetes patient data management.

PubMed

Deo, S S; Deobagkar, D N; Deobagkar, Deepti D

2005-01-01

A web-based database management system developed for collecting, managing and analysing information of diabetes patients is described here. It is a searchable, client-server, relational database application, developed on the Windows platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script. The software is menu-driven and allows authorized healthcare providers to access, enter, update and analyse patient information. Graphical representation of data can be generated by the system using bar charts and pie charts. An interactive web interface allows users to query the database and generate reports. Alpha- and beta-testing of the system was carried out and the system at present holds records of 500 diabetes patients and is found useful in diagnosis and treatment. In addition to providing patient data on a continuous basis in a simple format, the system is used in population and comparative analysis. It has proved to be of significant advantage to the healthcare provider as compared to the paper-based system.

SuperAGILE Services at ASDC

NASA Astrophysics Data System (ADS)

Preger, B.; Verrecchia, F.; Pittori, C.; Antonelli, L. A.; Giommi, P.; Lazzarotto, F.; Evangelista, Y.

2008-05-01

The Italian Space Agency Science Data Center (ASDC) is a facility with several responsibilities including support to all the ASI scientific missions as for management and archival of the data, acting as the interface between ASI and the scientific community and providing on-line access to the data hosted. In this poster we describe the services that ASDC provides for SuperAGILE, in particular the ASDC public web pages devoted to the dissemination of SuperAGILE scientific results. SuperAGILE is the X-Ray imager onboard the AGILE mission, and provides the scientific community with orbit-by-orbit information on the observed sources. Crucial source information including position and flux in chosen energy bands will be reported in the SuperAGILE public web page at ASDC. Given their particular interest, another web page will be dedicated entirely to GRBs and other transients, where new event alerts will be notified and where users will find all the available informations on the GRBs detected by SuperAGILE.