Ngu, A; Rocco, D; Critchlow, T; Buttler, D
The World Wide Web provides a vast resource to genomics researchers in the form of web-based access to distributed data sources--e.g. BLAST sequence homology search interfaces. However, the process for seeking the desired scientific information is still very tedious and frustrating. While there are several known servers on genomic data (e.g., GeneBank, EMBL, NCBI), that are shared and accessed frequently, new data sources are created each day in laboratories all over the world. The sharing of these newly discovered genomics results are hindered by the lack of a common interface or data exchange mechanism. Moreover, the number of autonomous genomics sources and their rate of change out-pace the speed at which they can be manually identified, meaning that the available data is not being utilized to its full potential. An automated system that can find, classify, describe and wrap new sources without tedious and low-level coding of source specific wrappers is needed to assist scientists to access to hundreds of dynamically changing bioinformatics web data sources through a single interface. A correct classification of any kind of Web data source must address both the capability of the source and the conversation/interaction semantics which is inherent in the design of the Web data source. In this paper, we propose an automatic approach to classify Web data sources that takes into account both the capability and the conversational semantics of the source. The ability to discover the interaction pattern of a Web source leads to increased accuracy in the classification process. At the same time, it facilitates the extraction of process semantics, which is necessary for the automatic generation of wrappers that can interact correctly with the sources.
James F. Aiton
Full Text Available The rapid expansion occurring in World-Wide Web activity is beginning to make the concepts of ‘global hypermedia’ and ‘universal document readership’ realistic objectives of the new revolution in information technology. One consequence of this increase in usage is that educators and students are becoming more aware of the diversity of the knowledge base which can be accessed via the Internet. Although computerised databases and information services have long played a key role in bioinformatics these same resources can also be used to provide core materials for teaching and learning. The large datasets and arch ives th at have been compiled for biomedical research can be enhanced with the addition of a variety of multimedia elements (images. digital videos. animation etc.. The use of this digitally stored information in structured and self-directed learning environments is likely to increase as activity across World-Wide Web increases.
Neerincx, Pieter B T; Leunissen, Jack A M
Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines.
Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P
Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.
Interfacing to the Web or programming interfaces for the Web is used to provide dynamic information for Web users. Using the Web as a transport system of information poses three constraints: namespace, statelessness and performance. To build interfaces on either server or client side of the Web one has to meet these constraints. Several examples, currently in use in High Energy Physics Experiments are described. They range from an interface to show where buildings are located to an interface showing active values of the On-line System of the DELPHI (CERN)..
Cheung David W
Full Text Available Abstract Background Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1 the platforms on which the applications run are heterogeneous, 2 their web interface is not machine-friendly, 3 they use a non-standard format for data input and output, 4 they do not exploit standards to define application interface and message exchange, and 5 existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates
Full Text Available Abstract The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS, adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded and http://soap.g-language.org/kbws_dl.wsdl (Document/literal.
Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru
The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).
McWilliam, Hamish; Valentin, Franck; Goujon, Mickael; Li, Weizhong; Narayanasamy, Menaka; Martin, Jenny; Miyar, Teresa; Lopez, Rodrigo
The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009-2010.
Full Text Available Abstract Background Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. Results To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. Conclusions The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others.
Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas
Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.
Neerincx, P.B.T.; Leunissen, J.A.M.
Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformatic
Xiao Li; Yizheng Zhang
It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biological data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium)and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.
Hekkelman, M L; Te Beek, T A H; Pettifer, S R; Thorne, D; Attwood, T K; Vriend, G
The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.
Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel,; Shibuya, Tetsuo
We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic ...
Rocco, D; Critchlow, T J
The World Wide Web provides an incredible resource to genomics researchers in the form of dynamic data sources--e.g. BLAST sequence homology search interfaces. The growth rate of these sources outpaces the speed at which they can be manually classified, meaning that the available data is not being utilized to its full potential. Existing research has not addressed the problems of automatically locating, classifying, and integrating classes of bioinformatics data sources. This paper presents an overview of a system for finding classes of bioinformatics data sources and integrating them behind a unified interface. We examine an approach to classifying these sources automatically that relies on an abstract description format: the service class description. This format allows a domain expert to describe the important features of an entire class of services without tying that description to any particular Web source. We present the features of this description format in the context of BLAST sources to show how the service class description relates to Web sources that are being described. We then show how a service class description can be used to classify an arbitrary Web source to determine if that source is an instance of the described service. To validate the effectiveness of this approach, we have constructed a prototype that can correctly classify approximately two-thirds of the BLAST sources we tested. We then examine these results, consider the factors that affect correct automatic classification, and discuss future work.
Casajus Ramo, A [University of Barcelona, Diagonal 647, ES-08028 Barcelona (Spain); Sapunov, M, E-mail: firstname.lastname@example.org [Centre de Physique des Particules de Marseille, 163 Av de Luminy Case 902 13288 Marseille (France)
Traditionally the interaction between users and the Grid is done with command line tools. However, these tools are difficult to use by non-expert users providing minimal help and generating outputs not always easy to understand especially in case of errors. Graphical User Interfaces are typically limited to providing access to the monitoring or accounting information and concentrate on some particular aspects failing to cover the full spectrum of grid control tasks. To make the Grid more user friendly more complete graphical interfaces are needed. Within the DIRAC project we have attempted to construct a Web based User Interface that provides means not only for monitoring the system behavior but also allows to steer the main user activities on the grid. Using DIRAC's web interface a user can easily track jobs and data. It provides access to job information and allows performing actions on jobs such as killing or deleting. Data managers can define and monitor file transfer activity as well as check requests set by jobs. Production managers can define and follow large data productions and react if necessary by stopping or starting them. The Web Portal is build following all the grid security standards and using modern Web 2.0 technologies which allow to achieve the user experience similar to the desktop applications. Details of the DIRAC Web Portal architecture and User Interface will be presented and discussed.
Full Text Available 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.
Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo
The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794
Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J; Claros, M Gonzalo; Trelles, Oswaldo
The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user's tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/.
Kalas, M.; Puntervoll, P.; Joseph, A.;
Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use...... and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth...... interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web....
Katayama, Toshiaki; Nakao, Mitsuteru; Takagi, Toshihisa
Web services have become widely used in bioinformatics analysis, but there exist incompatibilities in interfaces and data types, which prevent users from making full use of a combination of these services. Therefore, we have developed the TogoWS service to provide an integrated interface with advanced features. In the TogoWS REST (REpresentative State Transfer) API (application programming interface), we introduce a unified access method for major database resources through intuitive URIs that can be used to search, retrieve, parse and convert the database entries. The TogoWS SOAP API resolves compatibility issues found on the server and client-side SOAP implementations. The TogoWS service is freely available at: http://togows.dbcls.jp/.
Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo
We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.
Liu, Xiaoqiao; Wu, Jianmin; Wang, Jun; Liu, Xiaochuan; Zhao, Shuqi; Li, Zhe; Kong, Lei; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge
With the rapid progress of biological research, great demands are proposed for integrative knowledge-sharing systems to efficiently support collaboration of biological researchers from various fields. To fulfill such requirements, we have developed a data-centric knowledge-sharing platform WebLab for biologists to fetch, analyze, manipulate and share data under an intuitive web interface. Dedicated space is provided for users to store their input data and analysis results. Users can upload local data or fetch public data from remote databases, and then perform analysis using more than 260 integrated bioinformatic tools. These tools can be further organized as customized analysis workflows to accomplish complex tasks automatically. In addition to conventional biological data, WebLab also provides rich supports for scientific literatures, such as searching against full text of uploaded literatures and exporting citations into various well-known citation managers such as EndNote and BibTex. To facilitate team work among colleagues, WebLab provides a powerful and flexible sharing mechanism, which allows users to share input data, analysis results, scientific literatures and customized workflows to specified users or groups with sophisticated privilege settings. WebLab is publicly available at http://weblab.cbi.pku.edu.cn, with all source code released as Free Software.
Hildebrand, M.; Ossenbruggen, J.R. van
We demonstrate how to develop Web-based user interfaces for Semantic Web applications using commonly available, off-the-shelf Web widget libraries. By formally defining the underlying data model that is assumed by these widgets, Semantic Web application developers can use familiar RDF constructs to
Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo
Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
Willighagen Egon L
Full Text Available Abstract Background Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP and REpresentational State Transfer (REST services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use. Results We present a novel approach based on the open standard Extensible Messaging and Presence Protocol (XMPP, consisting of an extension (IO Data to comprise discovery, asynchronous invocation, and definition of data types in the service. That XMPP cloud services are capable of asynchronous communication implies that clients do not have to poll repetitively for status, but the service sends the results back to the client upon completion. Implementations for Bioclipse and Taverna are presented, as are various XMPP cloud services in bio- and cheminformatics. Conclusion XMPP with its extensions is a powerful protocol for cloud services that demonstrate several advantages over traditional HTTP-based Web services: 1 services are discoverable without the need of an external registry, 2 asynchronous invocation eliminates the need for ad-hoc solutions like polling, and 3 input and output types defined in the service allows for generation of clients on the fly without the need of an external semantics description. The many advantages over existing technologies make XMPP a highly interesting candidate for next generation online services in bioinformatics.
Full Text Available Abstract Background The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. Results This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA of the Object Management Group (OMG, we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. Conclusion MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository
Hekkelman, M.L.; Beek, T.A.H. te; Pettifer, S.R.; Thorne, D.; Attwood, T.K.; Vriend, G.
The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of p
DUAN Lei; SHEN Liren
Web services is used in Experimental Physics and Industrial Control System (EPICS). Combined with EPICS Channel Access protocol, Web services' high usability, platform independence and language independence can be used to design a fully transparent and uniform software interface layer, which helps us complete channel data acquisition, modification and monitoring functions. This software interface layer, a cross-platform of cross-language,has good interopcrability and reusability.
Baldi, Pierre; Brunak, Søren
, and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...... as a strategic frontier between biology and computer science. Machine learning approaches (e.g. neural networks, hidden Markov models, and belief networsk) are ideally suited for areas in which there is a lot of data but little theory. The goal in machine learning is to extract useful information from a body...... of data by building good probabilistic models. The particular twist behind machine learning, however, is to automate the process as much as possible.In this book, the authors present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological...
Katayama, T.; Arakawa, K.; Nakao, M.; Prins, J.C.P.
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, vario
Bassil, Youssef; 10.5121/ijwest.2012.3104
Recent advances in computing systems have led to a new digital era in which every area of life is nearly interrelated with information technology. However, with the trend towards large-scale IT systems, a new challenge has emerged. The complexity of IT systems is becoming an obstacle that hampers the manageability, operability, and maintainability of modern computing infrastructures. Autonomic computing popped up to provide an answer to these ever-growing pitfalls. Fundamentally, autonomic systems are self-configuring, self-healing, self-optimizing, and self-protecting; hence, they can automate all complex IT processes without human intervention. This paper proposes an autonomic HTML web-interface generator based on XML Schema and Style Sheet specifications for self-configuring graphical user interfaces of web applications. The goal of this autonomic generator is to automate the process of customizing GUI web-interfaces according to the ever-changing business rules, policies, and operating environment with th...
Andrei Maciuca; Dan Popescu
The current paper proposes a smart web interface designed for monitoring the status of the elderly people. There are four main user types used in the web application: the administrator (who has power access to all the application’s functionalities), the patient (who has access to his own personal data, like parameters history, personal details), relatives of the patient (who have administrable access to the person in care, access that is defined by the patient) and the medic (who can view ...
Tomatis, N.; Moreau, B.
The Autonomous Systems Lab at the Swiss Federal Institute of Technology Lausanne (EPFL) is engaged in mobile robotics research. The labs research focuses mainly on indoor localization and map building, outdoor locomotion and navigation, and micro mobile robotics. In the framework of a research project on mobile robot localization, a graphical web interface for our indoor robots has been developed. The purpose of this interface is twofold: it serves as a tool for task supervision for the rese...
WebFTS is a web-delivered file transfer and management solution which allows users to invoke reliable, managed data transfers on distributed infrastructures. The fully open source solution offers a simple graphical interface through which the power of the FTS3 service can be accessed without the installation of any special grid tools. Created following simplicity and efficiency criteria, WebFTS allows the user to access and interact with multiple grid and cloud storage. The “transfer engine” used is FTS3, the service responsible for distributing the majority of LHC data across WLCG infrastructure. This provides WebFTS with reliable, multi-protocol, adaptively optimised data transfers.The talk will focus on the recent development which allows transfers from/to Dropbox and CERNBox (CERN ownCloud deployment)
Full Text Available Data collection is a key component of an information system. The widespread penetration of ICT tools in organizations and institutions has resulted in a shift in the way the data is collected. Data may be collected in printed-form, by e-mails, on a compact disk, or, by direct upload on the management information system. Since web services are platform-independent, it can access data stored in the XML format from any platform. In this paper, we present an interface which uses web services for data collection. It requires interaction between a web service deployed for the purposes of data collection, and the web address where the data is stored. Our interface requires that the web service has pre-knowledge of the address from where the data is to be collected. Also, the data to be accessed must be stored in XML format. Since our interface uses computer-supported interaction on both sides, it eases the task of regular and ongoing data collection. We apply our framework to the Education Management Information System, which collects data from schools spread across the country.
Full Text Available This paper discusses a generic user interface for managing web data that is incorporated in a content management system. The interface is created at run-time from a set of XML documents stored in database. We accentuate the importance of content analysis phase that leads to a well formed data model. Another important aspect is the use of context in the interface and the hierarchical model to represent multiple relationships between hierarchy items. The proposed event model acts like a glue between data management and application logic.
Huynh, Tien; Rigoutsos, Isidore
In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple s...
The present paper covers a generic and dynamic framework for the web publishing of bioinformatics databases based upon a meta data design, Java Bean, Java Server Page(JSP), Extensible Markup Language(XML), Extensible Stylesheet Language(XSL) and Extensible Stylesheet Language Transformation(XSLT). In this framework, the content is stored in a configurable and structured XML format, dynamically generated from an Oracle Relational Database Management System(RDBMS). The presentation is dynamically generated by transforming the XML document into HTML through XSLT.This clean separation between content and presentation makes the web publishing more flexible; changing the presentation only needs a modification of the Extensive Stylesheet(XS).
Dragut, Eduard C; Yu, Clement T
There are millions of searchable data sources on the Web and to a large extent their contents can only be reached through their own query interfaces. There is an enormous interest in making the data in these sources easily accessible. There are primarily two general approaches to achieve this objective. The first is to surface the contents of these sources from the deep Web and add the contents to the index of regular search engines. The second is to integrate the searching capabilities of these sources and support integrated access to them. In this book, we introduce the state-of-the-art tech
McHenry, K.; Kooper, R.; Serbin, S. P.; LeBauer, D. S.; Desai, A. R.; Dietze, M. C.
We have developed the Predictive Ecosystem Analyzer (PEcAn) as an open-source scientific workflow system and ecoinformatics toolbox that manages the flow of information in and out of regional-scale terrestrial biosphere models, facilitates heterogeneous data assimilation, tracks data provenance, and enables more effective feedback between models and field research. The over-arching goal of PEcAn is to make otherwise complex analyses transparent, repeatable, and accessible to a diverse array of researchers, allowing both novice and expert users to focus on using the models to examine complex ecosystems rather than having to deal with complex computer system setup and configuration questions in order to run the models. Through the developed web interface we hide much of the data and model details and allow the user to simply select locations, ecosystem models, and desired data sources as inputs to the model. Novice users are guided by the web interface through setting up a model execution and plotting the results. At the same time expert users are given enough freedom to modify specific parameters before the model gets executed. This will become more important as more and more models are added to the PEcAn workflow as well as more and more data that will become available as NEON comes online. On the backend we support the execution of potentially computationally expensive models on different High Performance Computers (HPC) and/or clusters. The system can be configured with a single XML file that gives it the flexibility needed for configuring and running the different models on different systems using a combination of information stored in a database as well as pointers to files on the hard disk. While the web interface usually creates this configuration file, expert users can still directly edit it to fine tune the configuration.. Once a workflow is finished the web interface will allow for the easy creation of plots over result data while also allowing the user to
Kabisch, Thomas; Dragut, Eduard; Yu, Clement; Leser, Ulf
Much data in the Web is hidden behind Web query interfaces. In most cases the only means to "surface" the content of a Web database is by formulating complex queries on such interfaces. Applications such as Deep Web crawling and Web database integration require an automatic usage of these interfaces. Therefore, an important problem to be addressed is the automatic extraction of query interfaces into an appropriate model. We hypothesize the existence of a set of domain-independent "commonsense...
Pritychenko,B.; Sonzogni, A.A.
We present Sigma Web interface which provides user-friendly access for online analysis and plotting of the evaluated and experimental nuclear reaction data stored in the ENDF-6 and EXFOR formats. The interface includes advanced browsing and search capabilities, interactive plots of cross sections, angular distributions and spectra, nubars, comparisons between evaluated and experimental data, computations for cross section data sets, pre-calculated integral quantities, neutron cross section uncertainties plots and visualization of covariance matrices. Sigma is publicly available at the National Nuclear Data Center website at http://www.nndc.bnl.gov/sigma.
Johnson, Mark; Zaretskaya, Irena; Raytselis, Yan; Merezhuk, Yuri; McGinnis, Scott; Madden, Thomas L
Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement.
The purpose of this thesis was to develop a solution to display tensiomyographic measurements. The web application enables the user to access the measurement data stored in the cloud database. The open source Laravel framework written in the PHP programming language was used for developing the web interface. The architecture of the whole system and the web app user interface are introduced in more details. The main app functionalities and the way of using the web interface are also descri...
Full Text Available Abstract 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.
Oliver, J; Pisano, M E; Alonso, T; Roca, P
Statistics provides essential tool in Bioinformatics to interpret the results of a database search or for the management of enormous amounts of information provided from genomics, proteomics and metabolomics. The goal of this project was the development of a software tool that would be as simple as possible to demonstrate the use of the Bioinformatics statistics. Computer Simulation Methods (CSMs) developed using Microsoft Excel were chosen for their broad range of applications, immediate and easy formula calculation, immediate testing and easy graphics representation, and of general use and acceptance by the scientific community. The result of these endeavours is a set of utilities which can be accessed from the following URL: http://gmein.uib.es/bioinformatica/statistics. When tested on students with previous coursework with traditional statistical teaching methods, the general opinion/overall consensus was that Web-based instruction had numerous advantages, but traditional methods with manual calculations were also needed for their theory and practice. Once having mastered the basic statistical formulas, Excel spreadsheets and graphics were shown to be very useful for trying many parameters in a rapid fashion without having to perform tedious calculations. CSMs will be of great importance for the formation of the students and professionals in the field of bioinformatics, and for upcoming applications of self-learning and continuous formation.
Full Text Available Bioinformatics tools have gained popularity in biology but little is known about their validity. We aimed to assess the early contribution of 415 single nucleotide polymorphisms (SNPs associated with eight cardio-metabolic traits at the genome-wide significance level in adults in the Family Atherosclerosis Monitoring In earLY Life (FAMILY birth cohort. We used the popular web-based tool SNAP to assess the availability of the 415 SNPs in the Illumina Cardio-Metabochip genotyped in the FAMILY study participants. We then compared the SNAP output with the Cardio-Metabochip file provided by Illumina using chromosome and chromosomal positions of SNPs from NCBI Human Genome Browser (Genome Reference Consortium Human Build 37. With the HapMap 3 release 2 reference, 201 out of 415 SNPs were reported as missing in the Cardio-Metabochip by the SNAP output. However, the Cardio-Metabochip file revealed that 152 of these 201 SNPs were in fact present in the Cardio-Metabochip array (false negative rate of 36.6%. With the more recent 1000 Genomes Project release, we found a false-negative rate of 17.6% by comparing the outputs of SNAP and the Illumina product file. We did not find any 'false positive' SNPs (SNPs specified as available in the Cardio-Metabochip by SNAP, but not by the Cardio-Metabochip Illumina file. The Cohen's Kappa coefficient, which calculates the percentage of agreement between both methods, indicated that the validity of SNAP was fair to moderate depending on the reference used (the HapMap 3 or 1000 Genomes. In conclusion, we demonstrate that the SNAP outputs for the Cardio-Metabochip are invalid. This study illustrates the importance of systematically assessing the validity of bioinformatics tools in an independent manner. We propose a series of guidelines to improve practices in the fast-moving field of bioinformatics software implementation.
Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J.; Davenport, Karen W.; Bishop-Lilly, Kimberly A.; Xu, Yan; Ahmed, Sanaa; Feng, Shihai; Mokashi, Vishwesh P.; Chain, Patrick S.G.
Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. PMID:27899609
This Bachelor thesis provides an overview of different techniques used for web pages or web applications user interface development using Google Web Toolkit. During development process programmer and designer encounter the problem in which way should design be passed from designer to programmer. Designer can plot web page design easily on paper or in an appropriate program and sends it to the programmer. Or he can create design in more advanced form, as a multitude of different files. Prog...
Full Text Available Abstract Background The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Results Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i a workflow to annotate 100,000 sequences from an invertebrate species; ii an integrated system for analysis of the transcription factor binding sites (TFBSs enriched based on differential gene expression data obtained from a microarray experiment; iii a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Conclusions Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i the absence of several useful data or analysis functions in the Web service "space"; ii the lack of documentation of methods; iii lack of
Gutiérrez, Yoan; Fernández Martínez, Javier; Martinez-Barco, Patricio; Llopis, Fernando; Muñoz, Rafael; Díez, Alvaro
Social Analytics Web Interface es una aplicación web que permite visualizar y gestionar gráficas estadísticas avanzadas sobre contenido de las redes sociales tanto a nivel histórico como en tiempo real. Esto es posible gracias al consumo de servicios webs estándares que ofrecen metadatos sobre analítica social, como es el caso de Social Analytics Process (ver publicación en RUA). Social Analytics Web Interface ofrece a nivel general las siguientes funcionalidades: - Visualización de analít...
Dutta, S.; Prakash, S.; Estrada, D.; Pop, E.
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…
Huynh, Tien; Rigoutsos, Isidore
In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification--directly from sequence--of structural deviations from alpha-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.
Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson
This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with…
Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a…
Kuppusamy, K S; Aghila, G
Though World Wide Web is the single largest source of information, it is ill-equipped to serve the people with vision related problems. With the prolific increase in the interest to make the web accessible to all sections of the society, solving this accessibility problem becomes mandatory. This paper presents a technique for making web pages accessible for people with low vision issues. A model for making web pages accessible, WILI (Web Interface for people with Low-vision Issues) has been proposed. The approach followed in this work is to automatically replace the existing display style of a web page with a new skin following the guidelines given by Clear Print Booklet provided by Royal National Institute of Blind. "Single Click Solution" is one of the primary advantages provided by WILI. A prototype using the WILI model is implemented and various experiments are conducted. The results of experiments conducted on WILI indicate 82% effective conversion rate.
Full Text Available Abstract Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS and Computational Biology Research Center (CBRC and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.
Schmid Amy K
Full Text Available Abstract Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV, and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the
Hediger, Martin R; De Vico, Luca
We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. 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.
Daumke, Philipp; Schulz, Stefan; Markó, Kornél
Medical document retrieval presents a unique combination of challenges for the design and implementation of retrieval engines. We introduce a method to meet these challenges by implementing a multilingual retrieval interface for biomedical content in the World Wide Web. To this end we developed an automated method for interlingual query construction by which a standard Web search engine is enabled to process non-English queries from the biomedical domain in order to retrieve English documents.
Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro
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.
Full Text Available Upon the popularity of 3C devices, the visual creatures are all around us, such the online game, touch pad, video and animation. Therefore, the text-based web page will no longer satisfy users. With the popularity of webcam, digital camera, stereoscopic glasses, or head-mounted display, the user interface becomes more visual and multi-dimensional. For the consideration of 3D and visual display in the research of web user interface design, Augmented Reality technology providing the convenient tools and impressive effects becomes the hot topic. Augmented Reality effect enables users to represent parts of the digital objects on top of the physical surroundings. The easy operation with webcam greatly improving the visual representation of web pages becomes the interest of our research. Therefore, we apply Augmented Reality technology for developing a city tour web site to collect the opinions of users. Therefore, the website stickiness is an important measurement. The major tasks of the work include the exploration of Augmented Reality technology and the evaluation of the outputs of Augmented Reality. The feedback opinions of users are valuable references for improving AR application in the work. As a result, the AR increasing the visual and interactive effects of web page encourages users to stay longer and more than 80% of users are willing to return for visiting the website soon. Moreover, several valuable conclusions about Augmented Reality technology in web user interface design are also provided for further practical references.
Full Text Available The present article aims to describe a project consisting in designing a framework of applications used to create graphical interfaces with an Oracle distributed database. The development of the project supposed the use of the latest technologies: database Oracle server, Tomcat web server, JDBC (Java library used for accessing a database, JSP and Tag Library (for the development of graphical interfaces.
Lin, Ling; Zhou, Lizhu
Web databases provide different types of query interfaces to access the data records stored in the backend databases. While most existing works exploit a complex query interface with multiple input fields to perform schema identification of the Web databases, little attention has been paid on how to identify the schema of web databases by simple query interface (SQI), which has only one single query text input field. This paper proposes a new method of instance-based query probing to identify WDBs' interface and result schema for SQI. The interface schema identification problem is defined as generating the fullcondition query of SQI and a novel query probing strategy is proposed. The result schema is also identified based on the result webpages of SQI's full-condition query, and an extended identification of the non-query attributes is proposed to improve the attribute recall rate. Experimental results on web databases of online shopping for book, movie and mobile phone show that our method is effective and efficient.
Invenio is an open source web-based application that implements a digital library or document server, and it's used at CERN as the base of the CERN Document Server Institutional Repository and the Inspire High Energy Physics Subject Repository. The purpose of this work was to reimplement the administrative interface of the search engine in Invenio, using new and proved open source technologies, to simplify the code base and lay the foundations for the work that it will be done in porting the rest of the administrative interfaces to use these newer technologies. In my time as a CERN openlab summer student I was able to implement some of the features for the WebSearch Admin Interfaces, enhance some of the existing code with new features and find solutions to technical challenges that will be common when porting the other administrative interfaces modules.
Full Text Available C++ language was used for creating web applications at the department of Mapping and Cartography for many years. Plenty of projects started to be very large-scale and complicated to maintain. Consequently, the traditional way of adding functionality to a Web Server which previously has been used (CGI programs started being usefulness. I was looking for some solutions - particularly open source ones. I have tried many languages (solutions and finally I chose the Java language and started writing servlets. Using the Java language (servlets has significantly simplified the development of web applications. As a result, developing cycle was cut down. Because of Java JNI (Java Native Interface it is still possible to use C++ libraries which we are using. The main goal of this article is to share my practical experiences with rewriting typical CGI web application and creating complex geoinformatic web application.
Serban, Alexandru; Crisan-Vida, Mihaela; Mada, Leonard; Stoicu-Tivadar, Lacramioara
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.
LI Lin; SHEN Liren; ZHU Qing; WAN Tianmin
Accelerator database stores various static parameters and real-time data of accelerator. SSRF (Shanghai Synchrotron Radiation Facility) adopts relational database to save the data. We developed a data retrieval system based on XML Web Services for accessing the archive data. It includes a bottom layer interface and an interface applicable for accelerator physics. Client samples exemplifying how to consume the interface are given. The users can browse, retrieve and plot data by the client samples. Also, we give a method to test its stability. The test result and performance are described.
Franklin, Erik C; Stat, Michael; Pochon, Xavier; Putnam, Hollie M; Gates, Ruth D
The genus Symbiodinium encompasses a group of unicellular, photosynthetic dinoflagellates that are found free living or in hospite with a wide range of marine invertebrate hosts including scleractinian corals. We present GeoSymbio, a hybrid web application that provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium-host symbioses. The novelty of this application lies in the combination of a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or 'in the cloud' using Google Apps, and therefore does not require any specialty GIS, web programming or data programming expertise from the user. The current version of the application utilizes Symbiodinium data based on the ITS2 genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982-2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis. The application provides a unique tool set to facilitate research on the basic biology of Symbiodinium and expedite new insights into their ecology, biogeography and evolution in the face of a changing global climate. GeoSymbio can be accessed at https://sites.google.com/site/geosymbio/.
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.
Full Text Available The paper presents a monitoring solution for flow measurement through Web Dynpro ABAP interface. The use of integrated software systems in companies currently represents an essential condition for providing higher and more reliable access to information resources. The SAP Netweaver, a multilingual & multitasking system based on the three-tier client-server technology, is one of the mostly used integrated platforms implemented in companies.
Barker, T M; Young, J
Interactive documents for use with the World Wide Web have been developed for viewing multi-dimensional radiographic and visual images of human anatomy, derived from the Visible Human Project. Emphasis has been placed on user-controlled features and selections. The purpose was to develop an interface which was independent of host operating system and browser software which would allow viewing of information by multiple users. The interfaces were implemented using HyperText Markup Language (HTML) forms, C programming language and Perl scripting language. Images were pre-processed using ANALYZE and stored on a Web server in CompuServe GIF format. Viewing options were included in the document design, such as interactive thresholding and two-dimensional slice direction. The interface is an example of what may be achieved using the World Wide Web. Key applications envisaged for such software include education, research and accessing of information through internal databases and simultaneous sharing of images by remote computers by health personnel for diagnostic purposes.
Full Text Available One of the most important features which e-learning tools and environments must possess within the scope of lifelong learning is self-directed learning, which can be considered as a form of self-learning. The aim of this study was to determine, based on the views and recommendations of experts, interface design principles for the development of educational web interfaces that will support the self-directed learning of adults. This descriptive study was conducted with the contribution of 12 academicians specializing in interface design and self-directed learning. Within the scope of the study, new interfaces features were identified based on an evaluation of the literature on interface designs for self-directed learning, and the views of subject experts. Based on the study results, it was determined that interface designs supporting self-directed learning must possess five basic features, which include being user-directed, ensuring variety, being supported by learning analytics, being motivational, and being sharing-oriented.
Choi, Jeongseok; Kim, Jaekwon; Lee, Dong Kyun; Jang, Kwang Soo; Kim, Dai-Jin; Choi, In Young
Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA.
Thiel, William H; Giangrande, Paloma H
The development of DNA and RNA aptamers for research as well as diagnostic and therapeutic applications is a rapidly growing field. In the past decade, the process of identifying aptamers has been revolutionized with the advent of high-throughput sequencing (HTS). However, bioinformatics tools that enable the average molecular biologist to analyze these large datasets and expedite the identification of candidate aptamer sequences have been lagging behind the HTS revolution. The Galaxy Project was developed in order to efficiently analyze genome, exome, and transcriptome HTS data, and we have now applied these tools to aptamer HTS data. The Galaxy Project's public webserver is an open source collection of bioinformatics tools that are powerful, flexible, dynamic, and user friendly. The online nature of the Galaxy webserver and its graphical interface allow users to analyze HTS data without compiling code or installing multiple programs. Herein we describe how tools within the Galaxy webserver can be adapted to pre-process, compile, filter and analyze aptamer HTS data from multiple rounds of selection.
Fischer, Steve; Aurrecoechea, Cristina; Brunk, Brian P; Gao, Xin; Harb, Omar S; Kraemer, Eileen T; Pennington, Cary; Treatman, Charles; Kissinger, Jessica C; Roos, David S; Stoeckert, Christian J
Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy's flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org.
Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu
MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.
Garcia Montoro, Carlos; The ATLAS collaboration
The EventIndex project consists in the development and deployment of a complete catalogue of events for the ATLAS experiment at the LHC accelerator at CERN. In 2015 the ATLAS experiment has produced 12 billion real events in 1 million files, and 5 billion simulated events in 8 million files. The ATLAS EventIndex is running in production since mid- 2015, reliably collecting information worldwide about all produced events and storing them in a central Hadoop infrastructure. A subset of this information is copied to an Oracle relational database. These slides present two components of the ATLAS EventIndex: its data collection supervisor and its web interface partner.
Pritychenko,B.; Sonzogni, A.A.
The authors present Sigma, a Web-rich application which provides user-friendly access in processing and plotting of the evaluated and experimental nuclear reaction data stored in the ENDF-6 and EXFOR formats. The main interface includes browsing using a periodic table and a directory tree, basic and advanced search capabilities, interactive plots of cross sections, angular distributions and spectra, comparisons between evaluated and experimental data, computations between different cross section sets. Interactive energy-angle, neutron cross section uncertainties plots and visualization of covariance matrices are under development. Sigma is publicly available at the National Nuclear Data Center website at www.nndc.bnl.gov/sigma.
Manuel Juárez Pacheco
Full Text Available This paper describes a pilot study carried out to compare two Web interfaces used to support a collaborative learning design for science education. The study is part of a wider research project, which aims at characterizing computer software for collaborative learning in science education. The results coming from a questionnaire applied to teachers and researchers reveal the necessity to design technological tools based mainly on users’ needs and to take into account the impact of these tools on the learning of curricular contents.
Gelbart, Hadas; Brill, Gilat; Yarden, Anat
Providing learners with opportunities to engage in activities similar to those carried out by scientists was addressed in a web-based research simulation in genetics developed for high school biology students. The research simulation enables learners to apply their genetics knowledge while giving them an opportunity to participate in an authentic…
Mesbah, A.; Van Deursen, A.
Recently, a new web development technique for creating interactive web applications, dubbed AJAX, has emerged. In this new model, the single-page web interface is composed of individual components which can be updated/replaced independently. With the rise of AJAX web applications classical multi-pag
Ezra Tsur, Elishai
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.
Bayan Abu Shawar
Full Text Available In this paper, we describe a way to access Arabic Web Question Answering (QA corpus using a chatbot, without the need for sophisticated natural language processing or logical inference. Any Natural Language (NL interface to Question Answer (QA system is constrained to reply with the given answers, so there is no need for NL generation to recreate well-formed answers, or for deep analysis or logical inference to map user input questions onto this logical ontology; simple (but large set of pattern-template matching rules will suffice. In previous research, this approach works properly with English and other European languages. In this paper, we try to see how the same chatbot will react in terms of Arabic Web QA corpus. Initial results shows that 93% of answers were correct, but because of a lot of characteristics related to Arabic language, changing Arabic questions into other forms may lead to no answers.
Garcia Montoro, Carlos; The ATLAS collaboration; Sanchez, Javier
The EventIndex project consists in the development and deployment of a complete catalogue of events for the ATLAS experiment  at the LHC accelerator at CERN. In 2015 the ATLAS experiment has produced 12 billion real events in 1 million files, and 5 billion simulated events in 8 million files. The ATLAS EventIndex is running in production since mid-2015, reliably collecting information worldwide about all produced events and storing them in a central Hadoop infrastructure. A subset of this information is copied to an Oracle relational database. This paper presents two components of the ATLAS EventIndex : its data collection supervisor and its web interface partner.
Boughamoura, Radhouane; Omri, Mohamed Nazih
Deep Web databases contain more than 90% of pertinent information of the Web. Despite their importance, users don't profit of this treasury. Many deep web services are offering competitive services in term of prices, quality of service, and facilities. As the number of services is growing rapidly, users have difficulty to ask many web services in the same time. In this paper, we imagine a system where users have the possibility to formulate one query using one query interface and then the system translates query to the rest of query interfaces. However, interfaces are created by designers in order to be interpreted visually by users, machines can not interpret query from a given interface. We propose a new approach which emulates capacity of interpretation of users and extracts query from deep web query interfaces. Our approach has proved good performances on two standard datasets.
Beermann, Thomas; The ATLAS collaboration; Barisits, Martin-Stefan; Serfon, Cedric; Garonne, Vincent
Full Text Available Efficient delivery of relevant product information is increasingly becoming the central basis of competition between firms. The interface design represents the central component for successful information delivery to consumers. However, interface design for web-based information systems is probably more an art than a science at this point in time. Much research is needed to understand properties of an effective interface for electronic commerce. This paper develops a framework identifying the relationship between user factors, the role of the user interface and overall system success for web-based electronic commerce. The paper argues that web-based systems for electronic commerce have some similar properties to decision support systems (DSS and adapts an established DSS framework to the electronic commerce domain. Based on a limited amount of research studying web browser interface design, the framework identifies areas of research needed and outlines possible relationships between consumer characteristics, interface design attributes and measures of overall system success.
Raup, B.; Armstrong, R.; Fetterer, F.; Gartner-Roer, I.; Haeberli, W.; Hoelzle, M.; Khalsa, S. J. S.; Nussbaumer, S.; Weaver, R.; Zemp, M.
The Global Terrestrial Network for Glaciers (GTN-G) is an umbrella organization with links to the Global Climate Observing System (GCOS), Global Terrestrial Observing System (GTOS), and UNESCO (all organizations under the United Nations), for the curation of several glacier-related databases. It is composed of the World Glacier Monitoring Service (WGMS), the U.S. National Snow and Ice Data Center (NSIDC), and the Global Land Ice Measurements from Space (GLIMS) initiative. The glacier databases include the World Glacier Inventory (WGI), the GLIMS Glacier Database, the Glacier Photograph Collection at NSIDC, and the Fluctuations of Glaciers (FoG) and Mass Balance databases at WGMS. We are working toward increased interoperability between these related databases. For example, the Web interface to the GLIMS Glacier Database has also included queryable layers for the WGI and FoG databases since 2008. To improve this further, we have produced a new GTN-G web portal (http://www.gtn-g.org/), which includes a glacier metadata browsing application. This web application allows the browsing of the metadata behind the main GTN-G databases, as well as querying the metadata in order to get to the source, no matter which database holds the data in question. A new glacier inventory, called the Randolph Glacier Inventory 1.0, has recently been compiled. This compilation, which includes glacier outlines that do not have the attributes or IDs or links to other data like the GLIMS data do, was motivated by the tight deadline schedule of the sea level chapter of the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC). Now served from the GLIMS website (http://glims.org/), it is designed to serve that narrowly focused research goal in the near term, and in the longer term will be incorporated into the multi-temporal glacier database of GLIMS. For the required merging of large sets of glacier outlines and association of proper IDs that tie together outlines
Deep Web查询接口是Web数据库的接口,其对于Deep Web数据库集成至关重要.本文根据网页表单的结构特征定义查询接口；针对非提交查询法,给出界定Deep Web查询接口的一些规则；提出提交查询法,根据链接属性的特点进行判断,找到包含查询接口的页面；采用决策树C4.5算法进行分类,并用Java语言实现Deep Web查询接口系统.%Deep Web search interface is the interface of Web database. It is essential for the integration of Deep Web databases. According to the structural characteristics of the Web form, search interface is defined. For non-submission query method, some of the rules as defined in the Deep Web search interface are given. The submission query method is proposed, which finds out the page containing the search interface with the features of the link properties. The Web pages are classified with the C4. S decision tree algorithm, and the Deep Web search interface system is realized by using Java.
Full Text Available This paper deals with the Web Structure Mining and the different Structure Mining Algorithms like Page Rank, HITS, Trust Rank and Sel-HITS. The functioning of these algorithms are discussed. An incremental algorithm for calculation of PageRank using an interface has been formulated. This algorithm makes use of Web Link Attributes Information as key parameters and has been implemented using Visibility and Position of a Link. The application of Web Structure Mining Algorithm in an Academic Search Application has been discussed. The present work can be a useful input to Web Users, Faculty, Students and Web Administrators in a University Environment.
Odier, Jerome; The ATLAS collaboration; Fulachier, Jerome; Lambert, Fabian
Odier, J.; Albrand, S.; Fulachier, J.; Lambert, F.
Wallick, Michael N.; Doubleday, Joshua R.; Shams, Khawaja S.
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
Odier, Jerome; The ATLAS collaboration; Fulachier, Jerome; Lambert, Fabian
The ATLAS Metadata Interface (AMI) can be considered to be a mature application because it has existed for at least 10 years. Over the last year, we have been adapting the application to some recently available technologies. The web interface, which previously manipulated XML documents using XSL transformations, has been migrated to Asynchronous Java Script (AJAX). Web development has been considerably simplified by the development of a framework for AMI based on JQuery and Twitter Bootstrap. Finally there has been a major upgrade of the python web service client.
Eriksson, S. C.; Meertens, C. M.; Estey, L.; Weingroff, M.; Hamburger, M. W.; Holt, W. E.; Richard, G. A.
Papanicolaou, Alexie; Heckel, David G.
Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: email@example.com PMID:20971988
Boughamoura, Radhouane; Hlaoua, Lobna; Omri, Mohamed nazih
Deep Web databases contain more than 90% of pertinent information of the Web. Despite their importance, users don't profit of this treasury. Many deep web services are offering competitive services in term of prices, quality of service, and facilities. As the number of services is growing rapidly, users have difficulty to ask many web services in the same time. In this paper, we imagine a system where users have the possibility to formulate one query using one query interface and then the sys...
Zain, Jasni Mohamad; Goh, Yingsoon
Aesthetics of web page refers to how attractive a web page is in which it catches the attention of the user to read through the information. In addition, the visual appearance is important in getting attentions of the users. Moreover, it was found that those screens, which were perceived as aesthetically pleasing, were having a better usability. Usability might be a strong basic in relating to the applicability for learning, and in this study pertaining to Mandarin learning. It was also found that aesthetically pleasing layouts of web page would motivate students in Mandarin learning The Mandarin Learning web pages were manipulated according to the desired aesthetic measurements. GUI aesthetic measuring method was used for this purpose. The Aesthetics-Measurement Application (AMA) accomplished with six aesthetic measures was developed and used. On top of it, questionnaires were distributed to the users to gather information on the students' perceptions on the aesthetic aspects and learning aspects. Respondent...
熊岚; 胡洪良; 杜清运; 黄茂军; 王明军
The fusion of VISI (visual identity system Internet), digital maps and Web GIS is presented. Web GIS interface inter- active design with VISI needs to consider more new factors. VISI can provide the design principle, elements and contents for the Web GIS. The design of the Wuhan Bus Search System is fulfilled to confirm the validity and practicability of the fusion.
Full Text Available This research extends the capability for the new technology platform by Remote Data Inspection System (RDIS server from Furukawa Co., Ltd. Enabling the integration of standard Hypertext Markup Language (HTML programming and RDIS tag programming to create a user-friendly “point-and-click” web-based control mechanism. The integration allows the users to send commands to mobile robot over the Internet. Web-based control enables human to extend his action and intelligence to remote locations. Three mechanisms for web-based controls are developed: Manual remote control, continuous operation event and autonomous navigational control. In the manual remote control the user is fully responsible for the robot action and the robot do not use any sophisticated algorithms. The continuous operation event is the extension of the basic movement of a manual remote control mechanism. In the autonomous navigation control, the user has more flexibility to tell the robot to carry out specific tasks. Using this method, mobile robot can be controlled via the web, from any places connected to the network without constructing specific infrastructures for communication.
Devadason, Francis; Intaraksa, Neelawat; Patamawongjariya, Pornprapa; Desai, Kavita
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)
Jensen, Casper Svenning; Møller, Anders; Su, Zhendong
Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST). Conclusions The need for semantic integration technologies has preceded available solutions. We
Nelson Rex T
Full Text Available Abstract Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap" offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS] used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL, genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL, Resource Description Framework (RDF and eXtensible Markup Language (XML documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST. Conclusions The need for semantic integration technologies has preceded
Sharma, Parichit; Mantri, Shrikant S
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
Full Text Available 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
Reddy, Boojala Vijay B; Milshteyn, Aleksandr; Charlop-Powers, Zachary; Brady, Sean F
Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. Using PCR-generated sequence tags, the eSNaPD data-analysis pipeline profiles biosynthetic diversity hidden within (meta)genomes by comparing sequence tags to a reference data set of characterized gene clusters. Sample mapping, molecule discovery, library mapping, and new clade visualization modules facilitate the interrogation of large (meta)genomic sequence data sets for diverse downstream analyses, including, but not limited to, the identification of environments rich in untapped biosynthetic diversity, targeted molecule discovery efforts, and chemical ecology studies. eSNaPD is designed to generate a global atlas of biosynthetic diversity that can facilitate a systematic, sequence-based interrogation of nature's biosynthetic potential.
Wilkinson Mark D
Full Text Available Abstract Background User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins website. Results The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context. Conclusion This open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information.
Lauer, L.J.; Lynam, M.; Muniz, T. [Sandia National Labs., Albuquerque, NM (United States). Financial Systems Dept.
The Web Interface Template System (WITS) is a tool for software developers. WITS is a three-tiered, object-oriented system operating in a Client/Server environment. This tool can be used to create software applications that have a Web browser as the user interface and access a Sybase database. Development, modification, and implementation are greatly simplified because the developer can change and test definitions immediately, without writing or compiling any code. This document explains WITS functionality, the system structure and components of WITS, and how to obtain, install, and use the software system.
Manaud, N.; Gonzalez, J.
We present a first prototype of a Web Map Interface that will serve as a proof of concept and design for ESA's future fully web-based Planetary Science Archive (PSA) User Interface. The PSA is ESA's planetary science archiving authority and central repository for all scientific and engineering data returned by ESA's Solar System missions . All data are compliant with NASA's Planetary Data System (PDS) Standards and are accessible through several interfaces : in addition to serving all public data via FTP and the Planetary Data Access Protocol (PDAP), a Java-based User Interface provides advanced search, preview, download, notification and delivery-basket functionality. It allows the user to query and visualise instrument observations footprints using a map-based interface (currently only available for Mars Express HRSC and OMEGA instruments). During the last decade, the planetary mapping science community has increasingly been adopting Geographic Information System (GIS) tools and standards, originally developed for and used in Earth science. There is an ongoing effort to produce and share cartographic products through Open Geospatial Consortium (OGC) Web Services, or as standalone data sets, so that they can be readily used in existing GIS applications [3,4,5]. Previous studies conducted at ESAC [6,7] have helped identify the needs of Planetary GIS users, and define key areas of improvement for the future Web PSA User Interface. Its web map interface shall will provide access to the full geospatial content of the PSA, including (1) observation geometry footprints of all remote sensing instruments, and (2) all georeferenced cartographic products, such as HRSC map-projected data or OMEGA global maps from Mars Express. It shall aim to provide a rich user experience for search and visualisation of this content using modern and interactive web mapping technology. A comprehensive set of built-in context maps from external sources, such as MOLA topography, TES
Full Text Available Determining whether a site has a search interface is a crucial priority for further research of deep web databases. This study first reviews the current approaches employed in search interface identification for deep web databases. Then, a novel identification scheme using hybrid features and a feature-weighted instance-based learner is put forward. Experiment results show that the proposed scheme is satisfactory in terms of classification accuracy and our feature-weighted instance-based learner gives better results than classical algorithms such as C4.5, random forest and KNN.
Newman, R. L.; Clemesha, A.; Lindquist, K. G.; Reyes, J.; Steidl, J. H.; Vernon, F. L.
Robin Herlands Cresiski
Full Text Available Bioinformatics is becoming an important part of undergraduate curriculum, but expertise and well-evaluated teaching materials may not be available on every campus. Here, a guest speaker was utilized to introduce bioinformatics and web-available exercises were adapted for student investigation. Students used web-based nucleotide comparison tools to examine the medical and evolutionary relevance of a unidentified genetic sequence. Based on pre- and post-workshop surveys, there were significant gains in the students understanding of bioinformatics, as well as their perceived skills in using bioinformatics tools. The relevance of bioinformatics to a student’s career seemed dependent on career aspirations.
Parra Luzuriaga, Pablo Esteban
Este trabajo es una guía para el diseño y desarrollo de sitios Web Responsive para periódicos digitales, aquí se analizan las principales recomendaciones y buenas prácticas de expertos, más los principios del Diseño Centrado en el Usuario para formular una metodología de diseño que garantice los principios fundamentales de la Web Móvil: usabilidad, accesibilidad e interoperabilidad. Así mismo, para diseñar interfaces gráficas flexibles se analizaron diferentes metodologías de diseño Web Respo...
Zain, Jasni Mohamad; Goh, Yingsoon
This article describes the accurateness of our application namely Self-Developed Aesthetics Measurement Application (SDA) in measuring the aesthetics aspect by comparing the results of our application and users' perceptions in measuring the aesthetics of the web page interfaces. For this research, the positions of objects, images element and texts element are defined as objects in a web page interface. Mandarin learning web pages are used in this research. These learning web pages comprised of main pages, learning pages and exercise pages, on the first author's E-portfolio web site. The objects of the web pages were manipulated in order to produce the desired aesthetic values. The six aesthetics related elements used are balance, equilibrium, symmetry, sequence, rhythm, as well as order and complexity. Results from the research showed that the ranking of the aesthetics values of the web page interfaces measured of the users were congruent with the expected perceptions of our designed Mandarin learning web pag...
Firat, Mehmet; Sakar, A. Nurhan; Kabakci Yurdakul, Isil
One of the most important features which e-learning tools and environments must possess within the scope of lifelong learning is self-directed learning, which can be considered as a form of self-learning. The aim of this study was to determine, based on the views and recommendations of experts, interface design principles for the development of…
YUAN Fang; ZHAO Yao; ZHOU Xu
This paper proposes a new approach for classification for query interfaces of Deep Web, which extracts features from the form's text data on the query interfaces, assisted with the synonym library, and uses radial basic function neural network (RBFNN) algorithm to classify the query interfaces. The applied RBFNN is a kind of effective feed-forward artificial neural network, which has a simple networking structure but features with strength of excellent nonlinear approximation, fast convergence and global convergence. A TEL_8 query interfaces' data set from UIUC on-line database is used in our experiments, which consists of 477 query interfaces in 8 typical domains. Experimental results proved that the proposed approach can efficiently classify the query interfaces with an accuracy of 95.67%.
Tengku Siti Meriam Tengku Wook
Full Text Available There have been numerous studies done on the guidelines of user interface, but only a number of them have considered specific guidelines for the design of children’s interface. This paper is about a research on the specific guidelines for children, focusing on the criteria of graphic design. The objective of this research is to study on the guidelines of user interface design and to develop specific guidelines on children’s graphic design. The criteria of graphic design are the priority of this research since previous research have proven that graphic design is the main factor which contributes to the problem of usability of web application interfaces, in terms of the overall graphic layout not being in a hierarchical order, not taken into concern the availability of space, inappropriate margin, improper type and font size selection, and less concentration on the use of the colours. The research methodology makes use of the comparison of and the coordination to the guidelines on children’s interface and the specific guidelines on the graphic design of web application interfaces. The contribution of this research is the guidelines on the design of web application graphics which are specifically for children.
Knipp, D.; Kilcommons, L. M.; Damas, M. C.
We have created a simple and user-friendly web application to visualize output from empirical atmospheric models that describe the lower atmosphere and the Space-Atmosphere Interface Region (SAIR). The Atmospheric Model Web Explorer (AtModWeb) is a lightweight, multi-user, Python-driven application which uses standard web technology (jQuery, HTML5, CSS3) to give an in-browser interface that can produce plots of modeled quantities such as temperature and individual species and total densities of neutral and ionized upper-atmosphere. Output may be displayed as: 1) a contour plot over a map projection, 2) a pseudo-color plot (heatmap) which allows visualization of a variable as a function of two spatial coordinates, or 3) a simple line plot of one spatial coordinate versus any number of desired model output variables. The application is designed around an abstraction of an empirical atmospheric model, essentially treating the model code as a black box, which makes it simple to add additional models without modifying the main body of the application. Currently implemented are the Naval Research Laboratory NRLMSISE00 model for neutral atmosphere and the International Reference Ionosphere (IRI). These models are relevant to the Low Earth Orbit environment and the SAIR. The interface is simple and usable, allowing users (students and experts) to specify time and location, and choose between historical (i.e. the values for the given date) or manual specification of whichever solar or geomagnetic activity drivers are required by the model. We present a number of use-case examples from research and education: 1) How does atmospheric density between the surface and 1000 km vary with time of day, season and solar cycle?; 2) How do ionospheric layers change with the solar cycle?; 3 How does the composition of the SAIR vary between day and night at a fixed altitude?
Bruno, Andrew E; Soares, Alexei S; Owen, Robin L; Snell, Edward H
Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. The work presented here 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. In the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting information 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.
Groenewegen, D.M.; Visser, E.
This paper is a pre-print of: Danny M. Groenewegen, Eelco Visser. Integration of Data Validation and User Interface Concerns in a DSL for Web Applications. In Mark G. J. van den Brand, Jeff Gray, editors, Software Language Engineering, Second International Conference, SLE 2009, Denver, USA, October,
Discusses multimedia Web site design that may include images, animations, audio, and video. Highlights include interfaces that stress user-centered design; using only relevant media; placing high-demand content on secondary pages and keeping the home page simpler; providing information about the media; considering users with disabilities; and user…
Joan Segura Mora
Full Text Available BACKGROUND: It is well established that only a portion of residues that mediate protein-protein interactions (PPIs, the so-called hot spot, contributes the most to the total binding energy, and thus its identification is an important and relevant question that has clear applications in drug discovery and protein design. The experimental identification of hot spots is however a lengthy and costly process, and thus there is an interest in computational tools that can complement and guide experimental efforts. PRINCIPAL FINDINGS: Here, we present Presaging Critical Residues in Protein interfaces-Web server (http://www.bioinsilico.org/PCRPi, a web server that implements a recently described and highly accurate computational tool designed to predict critical residues in protein interfaces: PCRPi. PRCPi depends on the integration of structural, energetic, and evolutionary-based measures by using Bayesian Networks (BNs. CONCLUSIONS: PCRPi-W has been designed to provide an easy and convenient access to the broad scientific community. Predictions are readily available for download or presented in a web page that includes among other information links to relevant files, sequence information, and a Jmol applet to visualize and analyze the predictions in the context of the protein structure.
Full Text Available To surface the Deep Web, one crucial task is to predict whether a given web page has a search interface (searchable HyperText Markup Language (HTML form or not. Previous studies have focused on supervised classification with labeled examples. However, labeled data are scarce, hard to get and requires tediousmanual work, while unlabeled HTML forms are abundant and easy to obtain. In this research, we consider the plausibility of using both labeled and unlabeled data to train better models to identify search interfaces more effectively. We present a semi-supervised co-training ensemble learning approach using both neural networks and decision trees to deal with the search interface identification problem. We show that the proposed model outperforms previous methods using only labeled data. We also show that adding unlabeled data improves the effectiveness of the proposed model.
Hendry Setyawans Sutedjo
Full Text Available Informasi dalam sebuah website atau web diharapkan dapat sampaikan dan diterima oleh pencari informasi dengan mudah. Di dalam Dunia pendidikan, informasi yang ada di dalam web juga diharapkan mampu diterima oleh para penggunanya dengan tujuan media komunikasi online seperti website dapat membantu para pelajar menerima ilmu yang disampaikan melalui media online. Untuk Mengetahui seberapa mudahnya informasi itu ditangkap ditandai dengan seberapa mudah website itu digunakan (usable. Untuk mengetahui seberapa mudah penggunaan suatu website digunakan analisa usability, banyak metode yang dapat digunakan untuk mengidentifikasi masalah usability terutama dari sisi interface web. Heuristic evaluation merupakan salah satu teknik dalam melakukan hal tersebut yang digunakan dalam penelitian ini guna menilai seberapa mudahnya website Institut Teknologi Sepuluh Nopember dalam menyampaikan informasi yang ada. Dalam penelitian ini digunakan juga Quality Function Deployment (QFD untuk mengidentifikasi keinginan pengguna terhadap tampilan dari web ITS
Vali, Faisal; Hong, Robert
Full Text Available Abstract 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
Jeliazkova, Nina; Jeliazkov, Vedrin
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
利用文献计量学方法,统计分析了1995～2007 年Web of Science收录生物信息学数据库(bioinformatics databases)研究文献,探讨了生物信息学数据库文献研究的年代分布、语种、期刊分布、作者、文献类型、主题分布以及发文量前10名的国家和机构,以期了解世界各国在这一研究领域的进展情况.
Full Text Available This paper discusses the standards and guidelines of user interface features in web-based applications for the different personality types of people. An overview of human computer interaction and human personality types is described. LEONARD, Let’s Explore our personality type based on Openness (O, Neutral (N, Analytical (A, Relational (R and Decisive (D is the model used to determine the different personality types for this study. The purpose is to define user personality profiles and to establish guidelines for the graphical user interface. The personality inventory and a user interface questionnaire were administered to university students. Interview sessions were also conducted and parts of the interviews with the university students were used to validate the results obtained from the questionnaires. The analysis of the students' personality types identified five main groups. The results suggest that users do have definable expectations concerning the features of web applications. This profile served as basis for the guidelines of web features for the graphical user interface design for the particular user groups.
Lassnig, Mario; The ATLAS collaboration; Barisits, Martin-Stefan; Serfon, Cedric; Vigne, Ralph; Garonne, Vincent
The monitoring and controlling interfaces of the previous data management system DQ2 followed the evolutionary requirements and needs of the ATLAS collaboration. The new system, Rucio, has put in place a redesigned web-based interface based upon the lessons learnt from DQ2, and the increased volume of managed information. This interface encompasses both a monitoring and controlling component, and allows easy integration for user-generated views. The interface follows three design principles. First, the collection and storage of data from internal and external systems is asynchronous to reduce latency. This includes the use of technologies like ActiveMQ or Nagios. Second, analysis of the data into information is done massively parallel due to its volume, using a combined approach with an Oracle database and Hadoop MapReduce. Third, sharing of the information does not distinguish between human or programmatic access, making it easy to access selective parts of the information both in constrained frontends like ...
Lassnig, Mario; The ATLAS collaboration; Vigne, Ralph; Barisits, Martin-Stefan; Garonne, Vincent; Serfon, Cedric
The monitoring and controlling interfaces of the previous data management system DQ2 followed the evolutionary requirements and needs of the ATLAS collaboration. The new data management system, Rucio, has put in place a redesigned web-based interface based upon the lessons learnt from DQ2, and the increased volume of managed information. This interface encompasses both a monitoring and controlling component, and allows easy integration for user-generated views. The interface follows three design principles. First, the collection and storage of data from internal and external systems is asynchronous to reduce latency. This includes the use of technologies like ActiveMQ or Nagios. Second, analysis of the data into information is done massively parallel due to its volume, using a combined approach with an Oracle database and Hadoop MapReduce. Third, sharing of the information does not distinguish between human or programmatic access, making it easy to access selective parts of the information both in constrained...
Lange Ramos, Bruno; The ATLAS collaboration; Pommes, Kathy; Pavani Neto, Varlen; Vieira Arosa, Breno
In order to manage a heterogeneous and worldwide collaboration, the ATLAS experiment develops web systems that range from supporting the process of publishing scientific papers to monitoring equipment radiation levels. These systems are vastly supported by Glance, a technology that was set forward in 2004 to create an abstraction layer on top of varied databases that automatically recognizes their modeling and generate web search interfaces. Fence (Front ENd ENgine for glaNCE) assembles classes to build applications by making extensive use of configuration files. It produces templates of the core JSON files on top of which it is possible to create Glance-compliant search interfaces. Once the database, its schemas and tables are defined using Glance, its records can be incorporated into the templates by escaping the returned values with a reference to the column identifier wrapped around double enclosing brackets. The developer may also expand on available configuration files to create HTML forms and securely ...
Vernon, Frank; Newman, Robert; Lindquist, Kent
Cranford, Jonathan W.
The objective of this Langley Aerospace Research Summer Scholars (LARSS) research project was to write a user interface that utilizes current World Wide Web (WWW) technologies for an existing computer program written in C, entitled LaRCRisk. The project entailed researching data presentation and script execution on the WWW and than writing input/output procedures for the database management portion of LaRCRisk.
Langston, James H.; Murray, Henry L.; Hunt, Gary R.
A prototype has been developed which makes use of commercially available products in conjunction with the Java programming language to provide a secure user interface for command and control over the open Internet. This paper reports successful demonstration of: (1) Security over the Internet, including encryption and certification; (2) Integration of Java applets with a COTS command and control product; (3) Remote spacecraft commanding using the Internet. The Java-based Spacecraft Web Interface to Telemetry and Command Handling (Jswitch) ground system prototype provides these capabilities. This activity demonstrates the use and integration of current technologies to enable a spacecraft engineer or flight operator to monitor and control a spacecraft from a user interface communicating over the open Internet using standard World Wide Web (WWW) protocols and commercial off-the-shelf (COTS) products. The core command and control functions are provided by the COTS Epoch 2000 product. The standard WWW tools and browsers are used in conjunction with the Java programming technology. Security is provided with the current encryption and certification technology. This system prototype is a step in the direction of giving scientist and flight operators Web-based access to instrument, payload, and spacecraft data.
Lassnig, M.; Beermann, T.; Vigne, R.; Barisits, M.; Garonne, V.; Serfon, C.
The monitoring and controlling interfaces of the previous data management system DQ2 followed the evolutionary requirements and needs of the ATLAS collaboration. The new data management system, Rucio, has put in place a redesigned web-based interface based upon the lessons learnt from DQ2, and the increased volume of managed information. This interface encompasses both a monitoring and controlling component, and allows easy integration for usergenerated views. The interface follows three design principles. First, the collection and storage of data from internal and external systems is asynchronous to reduce latency. This includes the use of technologies like ActiveMQ or Nagios. Second, analysis of the data into information is done massively parallel due to its volume, using a combined approach with an Oracle database and Hadoop MapReduce. Third, sharing of the information does not distinguish between human or programmatic access, making it easy to access selective parts of the information both in constrained frontends like web-browsers as well as remote services. This contribution will detail the reasons for these principles and the design choices taken. Additionally, the implementation, the interactions with external systems, and an evaluation of the system in production, both from a technological and user perspective, conclude this contribution.
Martinez-Cagigal, Victor; Gomez-Pilar, Javier; Alvarez, Daniel; Hornero, Roberto
This paper presents an electroencephalographic (EEG) P300-based brain-computer interface (BCI) Internet browser. The system uses the "odd-ball" row-col paradigm for generating the P300 evoked potentials on the scalp of the user, which are immediately processed and translated into web browser commands. There were previous approaches for controlling a BCI web browser. However, to the best of our knowledge, none of them was focused on an assistive context, failing to test their applications with a suitable number of end users. In addition, all of them were synchronous applications, where it was necessary to introduce a "read-mode" command in order to avoid a continuous command selection. Thus, the aim of this study is twofold: (i) to test our web browser with a population of multiple sclerosis (MS) patients in order to assess the usefulness of our proposal to meet their daily communication needs; and (ii) to overcome the aforementioned limitation by adding a threshold that discerns between control and non-control states, allowing the user to calmly read the web page without undesirable selections. The browser was tested with sixteen MS patients and five healthy volunteers. Both quantitative and qualitative metrics were obtained. MS participants reached an average accuracy of 84.14%, whereas 95.75% was achieved by control subjects. Results show that MS patients can successfully control the BCI web browser, improving their personal autonomy.
Mateos, Cristian; Crasso, Marco; Rodriguez, Juan M.; Zunino, Alejandro; Campo, Marcelo
There is a good consensus on the strategic value of service-oriented architecture (SOA) as a way of structuring systems, and a common trend is to migrate legacy applications that use outdated technologies and architectures to SOA. We study the effects in the resulting Web Service interfaces of applying two traditional migration approaches combined with common ways of building services, namely, direct migration with code-first and indirect migration with contract-first. The migrated system was a 35-year-old COBOL system of a government agency that serves several millions of users. In addition, we provide a deep explanation of the trade-offs involved in following either combinations. Results confirm that the 'fast and cheap' approach to move into SOA, which is commonplace in the industry, may deliver poor service interfaces, and interface quality is also subject to the tools supporting the migration process.
Thomas A Schlacher
Full Text Available Food webs near the interface of adjacent ecosystems are potentially subsidised by the flux of organic matter across system boundaries. Such subsidies, including carrion of marine provenance, are predicted to be instrumental on open-coast sandy shores where in situ productivity is low and boundaries are long and highly permeable to imports from the sea. We tested the effect of carrion supply on the structure of consumer dynamics in a beach-dune system using broad-scale, repeated additions of carcasses at the strandline of an exposed beach in eastern Australia. Carrion inputs increased the abundance of large invertebrate scavengers (ghost crabs, Ocypode spp., a numerical response most strongly expressed by the largest size-class in the population, and likely due to aggregative behaviour in the short term. Consumption of carrion at the beach-dune interface was rapid and efficient, driven overwhelmingly by facultative avian scavengers. This guild of vertebrate scavengers comprises several species of birds of prey (sea eagles, kites, crows and gulls, which reacted strongly to concentrations of fish carrion, creating hotspots of intense scavenging activity along the shoreline. Detection of carrion effects at several trophic levels suggests that feeding links arising from carcasses shape the architecture and dynamics of food webs at the land-ocean interface.
Licurse, Mindy Y.; Cook, Tessa S.
Radiology and imaging informatics education have rapidly evolved over the past few decades. With the increasing recognition that future growth and maintenance of radiology practices will rely heavily on radiologists with fundamentally sound informatics skills, the onus falls on radiology residency programs to properly implement and execute an informatics curriculum. In addition, the American Board of Radiology may choose to include even more informatics on the new board examinations. However, the resources available for didactic teaching and guidance most especially at the introductory level are widespread and varied. Given the breadth of informatics, a centralized web-based interface designed to serve as an adjunct to standardized informatics curriculums as well as a stand-alone for other interested audiences is desirable. We present the development of a curriculum using PearlTrees, an existing web-interface based on the concept of a visual interest graph that allows users to collect, organize, and share any URL they find online as well as to upload photos and other documents. For our purpose, the group of "pearls" includes informatics concepts linked by appropriate hierarchal relationships. The curriculum was developed using a combination of our institution's current informatics fellowship curriculum, the Practical Imaging Informatics textbook1 and other useful online resources. After development of the initial interface and curriculum has been publicized, we anticipate that involvement by the informatics community will help promote collaborations and foster mentorships at all career levels.
Karp Peter D
Lange Ramos, Bruno; The ATLAS collaboration; Pommes, Kathy; Pavani Neto, Varlen; Vieira Arosa, Breno; Abreu Da Silva, Igor
The ATLAS Technical Coordination disposes of 17 Web systems to support its operation. These applications, whilst ranging from supporting the process of publishing scientific papers to monitoring radiation levels in the equipment at the cave, are constantly prone to changes in requirements due to the collaborative nature of the experiment and its management. In this context, a Web framework is proposed to unify the generation of the supporting interfaces. Fence assembles classes to build applications by making extensive use of JSON configuration files. It relies vastly on Glance, a technology that was set forth in 2003 to create an abstraction layer on top of the heterogeneous sources that store the technical coordination data. Once Glance maps out the database modeling, records can be referenced in the configuration files by wrapping unique identifiers around double enclosing brackets. The deployed content can be individually secured by attaching clearance attributes to their description thus ensuring that vi...
Avila Bravo, Carlos Julio
El Internet está experimentando un crecimiento cada vez mayor a nivel mundial, se va incrementando los niveles de velocidad y accesibilidad del mismo. A la par de este fenómeno global actualmente evidenciamos la evolución de las interfaces web que de cierto modo reflejan el crecimiento de Internet y la llamada Web 2.0. Así las interfaces hoy en día nos muestran las nuevas posibilidades y ventajas en cuanto a diseño, que llegaron de la mano de HTML5 (La más reciente actualización de HTML, el l...
Weber, Tilmann; Kim, Hyun Uk
. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http...
Harwood, A.; Lehmann Miotto, G.; Magnoni, L.; Vandelli, W.; Savu, D.
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
Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of scientific data between information resources difficu...
Trabant, C. M.; Ahern, T. K.; Stults, M.
At the IRIS Data Management Center (DMC) we have been developing web service data access interfaces for our, primarily seismological, repositories for five years. These interfaces have become the primary access mechanisms for all data extraction from the DMC. For the last two years the DMC has been a principal participant in the GeoWS project, which aims to develop common web service interfaces for data access across hydrology, geodesy, seismology, marine geophysics, atmospheric and other geoscience disciplines. By extending our approach we have converged, along with other project members, on a web service interface and presentation design appropriate for geoscience and other data. The key principles of the approach include using a simple subset of RESTful concepts, common calling conventions whenever possible, a common tabular text data set convention, human-readable documentation and tools to help scientific end users learn how to use the interfaces. The common tabular text format, called GeoCSV, has been incorporated into the DMC's seismic station and event (earthquake) services. In addition to modifying our existing services, we have developed prototype GeoCSV web services for data sets managed by external (unfunded) collaborators. These prototype services include interfaces for data sets at NGDC/NCEI (water level tides and meteorological satellite measurements), INTERMAGNET repository and UTEP gravity and magnetic measurements. In progress are interfaces for WOVOdat (volcano observatory measurements), NEON (ecological observatory measurements) and more. An important goal of our work is to build interfaces usable by non-technologist end users. We find direct usability by researchers to be a major factor in cross-discipline data use, which itself is a key to solving complex research questions. In addition to data discovery and collection by end users, these interfaces provide a foundation upon which federated data access and brokering systems are already being
Full Text Available Satellite data, radiative power of hot spots as measured with remote sensing, historical records, on site geological surveys, digital elevation model data, and simulation results together provide a massive data source to investigate the behavior of active volcanoes like Mount Etna (Sicily, Italy over recent times. The integration of these heterogeneous data into a coherent visualization framework is important for their practical exploitation. It is crucial to fill in the gap between experimental and numerical data, and the direct human perception of their meaning. Indeed, the people in charge of safety planning of an area need to be able to quickly assess hazards and other relevant issues even during critical situations. With this in mind, we developed LAV@HAZARD, a web-based geographic information system that provides an interface for the collection of all of the products coming from the LAVA project research activities. LAV@HAZARD is based on Google Maps application programming interface, a choice motivated by its ease of use and the user-friendly interactive environment it provides. In particular, the web structure consists of four modules for satellite applications (time-space evolution of hot spots, radiant flux and effusion rate, hazard map visualization, a database of ca. 30,000 lava-flow simulations, and real-time scenario forecasting by MAGFLOW on Compute Unified Device Architecture.
Oakley, N.; Daudert, B.
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.
Arakawa, Kazuharu; Kido, Nobuhiro; Oshita, Kazuki; Tomita, Masaru
G-language genome analysis environment (G-language GAE) contains more than 100 programs that focus on the analysis of bacterial genomes, including programs for the identification of binding sites by means of information theory, analysis of nucleotide composition bias and the distribution of particular oligonucleotides, calculation of codon bias and prediction of expression levels, and visualization of genomic information. We have provided a collection of web services for these programs by utilizing REST and SOAP technologies. The REST interface, available at http://rest.g-language.org/, provides access to all 145 functions of the G-language GAE. These functions can be accessed from other online resources. All analysis functions are represented by unique universal resource identifiers. Users can access the functions directly via the corresponding universe resource locators (URLs), and biological web sites can readily embed the functions by simply linking to these URLs. The SOAP services, available at http://www.g-language.org/wiki/soap/, provide language-independent programmatic access to 77 analysis programs. The SOAP service Web Services Definition Language file can be readily loaded into graphical clients such as the Taverna workbench to integrate the programs with other services and workflows.
Full Text Available Purpose: of this paper. The aim of this paper is to present a prototype of web-based programming interface for the Mitsubishi Movemaster RV-M1 robot.Design/methodology/approach: In the previous papers [11-14] the off-line, remote programming system for the mentioned robot has been presented. It has been used as a base for developing a new branch: web-based programming interface. The web techniques have been selected due to possibility of use existing code fragments for elaborating new applications and modularity of this solution.Findings: As a result, a prototype of the system has been developed.Research limitations/implications: Because the presented system is in the early development stage, there is a lack of some useful functions. Future work will include elaboration of the robot’s visualisation module and implementation of a trajectory translator intended to co-operate with CAD software.Practical implications: The elaborated system has been previously intended for educational purposes, but it may be adapted for other devices, like small PLC’s or other robots.Originality/value: Remote supervision of machines during a manufacturing process is an actual issue. Most of automation systems manufacturers produce software for their PLC’s and robots. Mitsubishi Movemaster RV-M1 is an old model and there is very few programs dedicated to this machine. On the other hand the programming and development of applications for this robot are very easy. The aim of the presented project is to develop a flexible, remote-programming environment.
Lange, Bruno; Maidantchik, Carmen; Pommes, Kathy; Pavani, Varlen; Arosa, Breno; Abreu, Igor
The ATLAS Technical Coordination disposes of 17 Web systems to support its operation. These applications, whilst ranging from managing the process of publishing scientific papers to monitoring radiation levels in the equipment in the experimental cavern, are constantly prone to changes in requirements due to the collaborative nature of the experiment and its management. In this context, a Web framework is proposed to unify the generation of the supporting interfaces. FENCE assembles classes to build applications by making extensive use of JSON configuration files. It relies heavily on Glance, a technology that was set forth in 2003 to create an abstraction layer on top of the heterogeneous sources that store the technical coordination data. Once Glance maps out the database modeling, records can be referenced in the configuration files by wrapping unique identifiers around double enclosing brackets. The deployed content can be individually secured by attaching clearance attributes to their description thus ensuring that view/edit privileges are granted to eligible users only. The framework also provides tools for securely writing into a database. Fully HTML5-compliant multi-step forms can be generated from their JSON description to assure that the submitted data comply with a series of constraints. Input validation is carried out primarily on the server- side but, following progressive enhancement guidelines, verification might also be performed on the client-side by enabling specific markup data attributes which are then handed over to the jQuery validation plug-in. User monitoring is accomplished by thoroughly logging user requests along with any POST data. Documentation is built from the source code using the phpDocumentor tool and made readily available for developers online. Fence, therefore, speeds up the implementation of Web interfaces and reduces the response time to requirement changes by minimizing maintenance overhead.
Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad
We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein–RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in ‘.pdb’ format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein–RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein–RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein–RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html. PMID:22689640
Kinzie, Mable B; Cohn, Wendy F; Julian, Marti F; Knaus, William A
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.
Golonka, Piotr; Fabian, Wojciech; Gonzalez-Berges, Manuel; Jasiun, Piotr; Varela-Rodriguez, Fernando
Harwood, A; The ATLAS collaboration; Lehmann Miotto, G
This paper describes a new approach to the visualization of stored 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 a posterior analysis. Although the ability to view these data-sets individually is already in place, there currently 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 diversely structured providers. It is capable of aggregating and correlating the data according to user defined criteria. Finally it v...
Full Text Available The Census of Population is one of the key sources of data for social science research in the UK. Many census results appear in published reports, but most data are available directly from the Office of National Statistics or from web sites offering extraction services for registered users. Many Geography students use information from the census to undertake projects and to complete dissertations, frequently when studying small geographical areas. It is important that students learn the skills for downloading census data and understand what shortcomings are associated with the data as well as knowing how to incorporate the data into GIS and to analyse it effectively. This paper focuses on how students at the University of Leeds are taught to use one particular product of the census, the Origin-Destination Statistics, that are available from a web-based interface known as WICID. The paper briefly outlines the context and characteristics of the data before explaining the rudiments of building queries and extracting data. A typical class assignment is presented to demonstrate how a student learns how to build queries using WICID before analysing the results or mapping the data using an independent GIS. Experience indicates that students need to think hard about their requirements before using WICID for project work.
Mandl, Daniel; Cappelaere, Pat; Frye, Stuart; Sohlberg, Rob; Ly, Vuong; Chien, Steve; Sullivan, Don
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.
Li, Liang-Yi; Chen, Gwo-Dong
Information Gathering is a knowledge construction process. Web learners make a plan for their Information Gathering task based on their prior knowledge. The plan is evolved with new information encountered and their mental model is constructed through continuously assimilating and accommodating new information gathered from different Web pages. In…
Full Text Available Abstract Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.
Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc
EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…
, and software are also key parts of flow cytometry bioinformatics. Data standards include the widely adopted Flow Cytometry Standard (FCS defining how data from cytometers should be stored, but also several new standards under development by the International Society for Advancement of Cytometry (ISAC to aid in storing more detailed information about experimental design and analytical steps. Open data is slowly growing with the opening of the CytoBank database in 2010 and FlowRepository in 2012, both of which allow users to freely distribute their data, and the latter of which has been recommended as the preferred repository for MIFlowCyt-compliant data by ISAC. Open software is most widely available in the form of a suite of Bioconductor packages, but is also available for web execution on the GenePattern platform.
Oostra, D.; Chambers, L. H.; Lewis, P. M.; Moore, S. W.
The Atmospheric Science Data Center (ASDC) at the NASA Langley Research Center in Virginia houses almost three petabytes of data, a collection that increases every day. To put it into perspective, it is estimated that three petabytes of data storage could store a digitized copy of all printed material in U.S. research libraries. There are more than ten other NASA data centers like the ASDC. Scientists and the public use this data for research, science education, and to understand our environment. Most importantly these data provide the potential for all of us make new discoveries. NASA is about making discoveries. Galileo was quoted as saying, "All discoveries are easy to understand once they are discovered. The point is to discover them." To that end, NASA stores vast amounts of publicly available data. This paper examines an approach to create web applications that serve NASA data in ways that specifically address the mobile web application technologies that are quickly emerging. Mobile data is not a new concept. What is new, is that user driven tools have recently become available that allow users to create their own mobile applications. Through the use of these cloud-based tools users can produce complete native mobile applications. Thus, mobile apps can now be created by everyone, regardless of their programming experience or expertise. This work will explore standards and methods for creating dynamic and malleable application programming interfaces (APIs) that allow users to access and use NASA science data for their own needs. The focus will be on experiences that broaden and increase the scope and usage of NASA science data sets.
Colini, L.; Doumaz, F.; Spinetti, C.; Mazzarini, F.; Favalli, M.; Isola, I.; Buongiorno, M. F.; Ananasso, C.
In the frame of the future Italian Space Agency (ASI) Space Mission PRISMA (Precursore IperSpettrale della Missione Applicativa), the Istituto Nazionale di Geofisica e Vulcanologia (INGV) coordinates the scientific project ASI-AGI (Analisi Sistemi Iperspettrali per le Applicazioni Geofisiche Integrate) aimed to study the hyperspectral volcanic applications and to identify and characterize a vicarious validation and calibration site for hyperspectral space missions. PRISMA is an Earth observation system with innovative electro-optical instrumentation which combines an hyperspectral sensor with a panchromatic medium-resolution camera. These instruments offer the scientific community and users many applications in the field of environmental monitoring, risk management, crop classification, pollution control, and Security. In this context Mt. Etna (Italy) has been choose as main site for testing the sensor capability to assess volcanic risk. The volcanic calibration and validation activities comprise the managing of a large amount of in situ hyperspectral data collected during the last 10 years. The usability and interoperability of these datasets represents a task of ASI-AGI project. For this purpose a database has been created to collect all the spectral signatures of the measured volcanic surfaces. This process has begun with the creation of the metadata structure compliant with those belonging to some standard spectral libraries such as USGS ones. Each spectral signature is described in a table containing ancillary data such as the location map of where it was collected, description of the target selected, etc. The relational database structure has been developed WOVOdat compliant. Specific tables have been formatted for each type of measurements, instruments and targets in order to query the database through a user-friendly web-interface. The interface has an upload area to populate the database and a visualization tool that allows downloading the ASCII spectral
Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee
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.
Li, Ping; Cunningham, Krystal
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.
Full Text Available Abstract Background Expressed sequence tag (EST collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation. Results We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval. Conclusion The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http
Mesbah, A.; Van Deursen, A.; Lenselink, S.
SHENG Qi-zheng; De Moor Bart
As a newborn interdisciplinary field, bioinformatics is receiving increasing attention from biologists, computer scientists, statisticians, mathematicians and engineers. This paper briefly introduces the birth, importance, and extensive applications of bioinformatics in the different fields of biological research. A major challenge in bioinformatics - the unraveling of gene regulation - is discussed in detail.
Full Text Available Critical human-machine interfaces are present in many systems including avionics systems and medical devices. Use error is a concern in these systems both in terms of hardware panels and input devices, and the software that drives the interfaces. Guaranteeing safe usability, in terms of buttons, knobs and displays is now a key element in the overall safety of the system. New integrated development environments (IDEs based on formal methods technologies have been developed by the research community to support the design and analysis of high-confidence human-machine interfaces. To date, little work has focused on the comparison of these particular types of formal IDEs. This paper compares and evaluates two state-of-the-art toolkits: CIRCUS, a model-based development and analysis tool based on Petri net extensions, and PVSio-web, a prototyping toolkit based on the PVS theorem proving system.
Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka
Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.
WebRTC provides a simple API for web browsers and mobile application to enable Real-Time Communications (RTC) in your application. In this talk we explore the technology roadmap, an overview of the main API functions and the elements needed to establish a peer-to-peer communication between two clients.
Finnerty, John R; Gilmore, Thomas D
Phylogenetic analysis enables one to reconstruct the functional evolution of proteins. Current understanding of NF-κB signaling derives primarily from studies of a relatively small number of laboratory models-mainly vertebrates and insects-that represent a tiny fraction of animal evolution. As such, NF-κB has been the subject of limited phylogenetic analysis. The recent discovery of NF-κB proteins in "basal" marine animals (e.g., sponges, sea anemones, corals) and NF-κB-like proteins in non-metazoan lineages extends the origin of NF-κB signaling by several hundred million years and provides the opportunity to investigate the early evolution of this pathway using phylogenetic approaches. Here, we describe a combination of bioinformatic and phylogenetic analyses based on menu-driven, open-source computer programs that are readily accessible to molecular biologists without formal training in phylogenetic methods. These phylogenetically based comparisons of NF-κB proteins are powerful in that they reveal deep conservation and repeated instances of parallel evolution in the sequence and structure of NF-κB in distant animal groups, which suggest that important functional constraints limit the evolution of this protein.
Abouelhoda, Mohamed; Ghanem, Moustafa
Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages , fighting spam mails , detecting plagiarism , and spotting duplications in software systems .
Glez-Peña, Daniel; Lourenço, Anália; López-Fernández, Hugo; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino
Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applications, ranging from simple extraction robots to online meta-servers. This article reviews existing scraping frameworks and tools, identifying their strengths and limitations in terms of extraction capabilities. The main focus is set on showing how straightforward it is today to set up a data scraping pipeline, with minimal programming effort, and answer a number of practical needs. For exemplification purposes, we introduce a biomedical data extraction scenario where the desired data sources, well-known in clinical microbiology and similar domains, do not offer programmatic interfaces yet. Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis.
The paper presents the necessity of implementing the government information public system interface based on web ser⁃vice. The web service interface system architecture and operation principle are introduced. The design and implementation of web service interface applied in the government information public system is also expounded in the paper. In addition, web service inter⁃face's application and prospects are suggested in sharing government information among government departments.%提出了基于Web Service的政府信息公开系统接口建设必要性，介绍了Web Service接口的体系架构和工作原理，详细阐述了政府信息公开系统Web Service接口的设计和实现过程。文章最后介绍了政府信息公开系统Web Service接口在推进政府部门的政务信息资源共享与服务中的应用及前景。
Kamel Boulos Maged N
Full Text Available Abstract Background On 21 July 2004, the Healthcare Commission http://www.healthcarecommission.org.uk/ released its annual star ratings of the performance of NHS Primary Care Trusts (PCTs in England for the year ending March 2004. The Healthcare Commission started work on 1 April 2004, taking over all the functions of the former Commission for Health Improvement http://www.chi.nhs.uk/, which had released the corresponding PCT ratings for 2002/2003 in July 2003. Results We produced two Web-based interactive maps of PCT star ratings, one for 2003 and the other for 2004 http://healthcybermap.org/PCT/ratings/, with handy functions like map search (by PCT name or part of it. The maps feature a colour-blind friendly quadri-colour scheme to represent PCT star ratings. Clicking a PCT on any of the maps will display the detailed performance report of that PCT for the corresponding year. Conclusion Using our Web-based interactive maps, users can visually appreciate at a glance the distribution of PCT performance across England. They can visually compare the performance of different PCTs in the same year and also between 2003 and 2004 (by switching between the synchronised 'PCT Ratings 2003' and 'PCT Ratings 2004' themes. The performance of many PCTs has improved in 2004, whereas some PCTs achieved lower ratings in 2004 compared to 2003. Web-based interactive geographical interfaces offer an intuitive way of indexing, accessing, mining, and understanding large healthcare information sets describing geographically differentiated phenomena. By acting as an enhanced alternative or supplement to purely textual online interfaces, interactive Web maps can further empower organisations and decision makers.
Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh
In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current res...
Shen, Siu-Tsen; Prior, Stephen D.; Chen, Kuen-Meau
This paper compares the perspicacity, appropriateness and preference of web browser icons from leading software providers with those of a culture-specific design. This online study was conducted in Taiwan and involved 103 participants, who were given three sets of web browser icons to review, namely Microsoft Internet Explorer, Macintosh Safari, and culturally specific icons created using the Culture-Centred Design methodology. The findings of the study show that all three sets have generally...
Polkowski, Marcin; Grad, Marek
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.
Full Text Available The paper treats the process of the creation of a web application optimal output for mobile devices in the form of a responsive layout with focus on the agrarian web portal. The utilization and testing of user experience (UX techniques in four steps - UX, research, design and testing - were of great benefit. Two groups of five people representing the task group were employed for the research and testing. The resulting responsive layout was developed with the emphasis on the ergonomic layout of control elements and content, a conservative design, the securing of content accessibility for disabled users and the possibility of fast and simple updating. The resulting knowledge is applicable to web information sources in the agrarian sector (agriculture, food industry, forestry, water supply and distribution and the development of rural areas. In wider context, this knowledge is valid in general.
Bland, Peyton H; Laderach, Gary E; Meyer, Charles R
Policies and regulations in the current health care environment have impacted the manner in which patient data - especially protected health information (PHI) - are handled in the clinical and research settings. Specifically, it is now more challenging to obtain de-identified PHI from the clinic for use in research while still adhering to the requirements dictated by the new policies and regulations. To meet this challenge, we have designed and implemented a novel web-based interface that uses a workflow model to manage the communication of data (for example, biopsy results) between the clinic and research environments without revealing PHI to the research team or associated research identifiers to the clinical collaborators. At the heart of the scheme is a web application that coordinates message passing between researchers and clinical collaborators by use of a protocol that protects confidentiality. We describe the design requirements of the messaging/communication protocol, as well as implementation details of the web application and its associated database. We conclude that this scheme provides a useful communication mechanism that facilitates clinical research while maintaining confidentiality of patient data.
En este trabajo nos enfocamos en desarrollar un prototipo para el sitio Web móvil de la Unidad Académica Caleta Olivia (UACO de la Universidad Nacional de la Patagonia Austral (UNPA considerando al usuario como el centro del diseño y desarrollo. Con esta filosofía en mente, se define un marco de trabajo para el desarrollo del prototipo incorporando recomendaciones de Usabilidad y Accesibilidad Web de referentes internacionales y aplicando herramientas para el diseño inclusivo dirigido a dispositivos móviles.
Computerens interface eller grænseflade har spredt sig overalt. Mobiltelefoner, spilkonsoller, pc'er og storskærme indeholder computere – men computere indbygges også i tøj og andre hverdagslige genstande, så vi konstant har adgang til digitale data. Interface retter fokus mod, hvordan den digita...
Matthew L. Clark
Full Text Available Web-based applications that integrate geospatial information, or the geoweb, offer exciting opportunities for remote sensing science. One such application is a Web‑based system for automating the collection of reference data for producing and verifying the accuracy of land-use/land-cover (LULC maps derived from satellite imagery. Here we describe the capabilities and technical components of the Virtual Interpretation of Earth Web-Interface Tool (VIEW-IT, a collaborative browser-based tool for “crowdsourcing” interpretation of reference data from high resolution imagery. The principal component of VIEW-IT is the Google Earth plug-in, which allows users to visually estimate percent cover of seven basic LULC classes within a sample grid. The current system provides a 250 m square sample to match the resolution of MODIS satellite data, although other scales could be easily accommodated. Using VIEW-IT, a team of 23 student and 7 expert interpreters collected over 46,000 reference samples across Latin America and the Caribbean. Samples covered all biomes, avoided spatial autocorrelation, and spanned years 2000 to 2010. By embedding Google Earth within a Web-based application with an intuitive user interface, basic interpretation criteria, distributed Internet access, server-side storage, and automated error-checking, VIEW-IT provides a time and cost efficient means of collecting a large dataset of samples across space and time. When matched with predictor variables from satellite imagery, these data can provide robust mapping algorithm calibration and accuracy assessment. This development is particularly important for regional to global scale LULC mapping efforts, which have traditionally relied on sparse sampling of medium resolution imagery and products for reference data. Our ultimate goal is to make VIEW-IT available to all users to promote rigorous, global land-change monitoring.
Biegert, Andreas; Mayer, Christian; Remmert, Michael; Söding, Johannes; Lupas, Andrei N
The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification. Several public tools are offered in customized versions that extend their functionality. For example, PSI-BLAST can be run against regularly updated standard databases, customized user databases or selectable sets of genomes. Another tool, Quick2D, integrates the results of various secondary structure, transmembrane and disorder prediction programs into one view. The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool. The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de.
Berrios, Daniel C.; Keller, Richard M.
While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.
Perri, M. J.; Weber, S. H.
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.
束长波; 施化吉; 王基
针对现有 Deep Web 信息集成系统没有考虑查询接口动态性的特点，造成本地接口与网络接口查询能力不对等的问题，提出一种基于演化版本的 Deep Web 查询接口维护方法。该方法通过构建本地接口的版本化模型来刻画接口的增量变化，识别变动比较活跃的属性集合；然后采取试探性查询来构建最优查询语句，获取网络接口数据源的变动信息，演化出本地接口的下一个版本，实现对本地查询接口数据源的信息维护的迭代过程。实验结果表明，该方法降低了深网环境变化对 Deep Web 信息集成带来的影响，确保了 Deep Web 查询接口的准确率和查全率的稳定性。%In order to solve the problems existed in the traditional Deep Web information integration system that without con-sidering the dynamic feature of search interface,causing local interface and network interface query ability is not equal.There-fore,this paper proposed a Deep Web search interface maintenance method based on evolution version.In this method,con-structing the version models of local search interface was to express the incremental change of it,and to extract the active attrib-ute set.Next,generating the best query string with the set and probing query was to extract the change content and get the next version of local interface.Finally,it could realize the iterative maintenance of local search interface data source.The experi-mental results show that this method is able to decrease the impact caused by deep Web network changing,and keep the recall and precision of Deep Web search interface in a stable state.
Network information era of rapid development of science and technology,Webpage interface design has been paid more attention to.Webpage interface become mediated interaction between the user and the computer, gets depends mainly on the Webpage interface information transmit visual information obtained from perception people outside information. Based on the Webpage interface design clarity, artistic, fluency, the rationality of the analysis and the discussion, think Webpage interface design must be humanized.%科技飞速发展的网络信息时代，网页界面设计日益得到重视。网页界面成为了用户与电脑之间互动的介体，人们对外界信息的获取主要靠网页界面信息的视觉信息传递获得感知。本文通过对网页界面设计的准确性、艺术性、流畅性、合理性进行了分析与探讨，认为网页界面设计必须人性化。
Full Text Available According to the advancement in internet and web-based application, the survey via the internet has been increasingly utilized due to its convenience and time saving. This article studied the influence of five web-design techniques - screen design, response format, logo type, progress indicator, and image display on the interest of the respondents. Two screen display designs from each design technique were made for selection. Focus group discussion technique was conducted on the four groups of Y generation participants with different characteristics. Open discussion was performed to identify additional design factors that will affect the interest of the questionnaire. The study found the degree of influence of all related design factors can be ranked from screen design, response format, font type, logo type, background color, progress indicator, and image display respectively.
the WWW interface. User WWW Server Keithley 2602 Nanotube, graphene or Intel CMOS erver GPIB it l 1 Nanotube, graphene or Si MOSFET Electrical...Educational technology, engineering education, MOSFETs , online services, transistors The authors are...and metal-oxide-semiconductor field effect transistors ( MOSFETs ). Theoretical studies alone cannot provide students with a complete understanding
Full Text Available Abstract Background To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes it difficult to find the right tool, or more importantly, the right set of tools that can work together to solve real complex problems. Results Magallanes (Magellan is a versatile, platform-independent Java library of algorithms aimed at discovering bioinformatics web services and associated data types. A second important feature of Magallanes is its ability to connect available and compatible web services into workflows that can process data sequentially to reach a desired output given a particular input. Magallanes' capabilities can be exploited both as an API or directly accessed through a graphic user interface. The Magallanes' API is freely available for academic use, and together with Magallanes application has been tested in MS-Windows™ XP and Unix-like operating systems. Detailed implementation information, including user manuals and tutorials, is available at http://www.bitlab-es.com/magallanes. Conclusion Different implementations of the same client (web page, desktop applications, web services, etc. have been deployed and are currently in use in real installations such as the National Institute of Bioinformatics (Spain and the ACGT-EU project. This shows the potential utility and versatility of the software library, including the integration of novel tools in the domain and with strong evidences in the line of facilitate the automatic discovering and composition of workflows.
Neugebauer, Tomasz; Bordeleau, Eric; Burrus, Vincent; Brzezinski, Ryszard
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.
Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh
In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.
The integration of services is transparent, meaning that users no longer face the millions of Web services, do not care about the required data stored, but do not need to learn how to obtain these data. In this paper, we analyze the uncertainty of schema matching, and then propose a series of similarity measures. To reduce the cost of execution, we propose the type-based optimization method and schema matching pruning method of numeric data. Based on above analysis, we propose the uncertain schema matching method. The experiments prove the effectiveness and efficiency of our method.
Maddox, Marlo; Zheng, Yihua; Rastaetter, Lutz; Taktakishvili, A.; Mays, M. L.; Kuznetsova, M.; Lee, Hyesook; Chulaki, Anna; Hesse, Michael; Mullinix, Richard; Berrios, David
The NASA GSFC Space Weather Center (http://swc.gsfc.nasa.gov) is committed to providing forecasts, alerts, research, and educational support to address NASA's space weather needs - in addition to the needs of the general space weather community. We provide a host of services including spacecraft anomaly resolution, historical impact analysis, real-time monitoring and forecasting, custom space weather alerts and products, weekly summaries and reports, and most recently - video casts. There are many challenges in providing accurate descriptions of past, present, and expected space weather events - and the Space Weather Center at NASA GSFC employs several innovative solutions to provide access to a comprehensive collection of both observational data, as well as space weather model/simulation data. We'll describe the challenges we've faced with managing hundreds of data streams, running models in real-time, data storage, and data dissemination. We'll also highlight several systems and tools that are utilized by the Space Weather Center in our daily operations, all of which are available to the general community as well. These systems and services include a web-based application called the Integrated Space Weather Analysis System (iSWA http://iswa.gsfc.nasa.gov), two mobile space weather applications for both IOS and Android devices, an external API for web-service style access to data, google earth compatible data products, and a downloadable client-based visualization tool.
Enhanced decision support for policy makers using a web interface to health-economic models - Illustrated with a cost-effectiveness analysis of nation-wide infant vaccination with the 7-valent pneumococcal conjugate vaccine in the Netherlands
Hubben, G.A.A.; Bos, J.M.; Glynn, D.M.; van der Ende, A.; van Alphen, L.; Postma, M.J.
We have developed a web-based user-interface (web interface) to enhance the usefulness of health-economic evaluations to support decision making (http://pcv.healtheconomics.nl). It allows the user to interact with a health-economic model to evaluate predefined and customized scenarios and perform se
van Hulst, Marinus; Hubben, Gijs A. A.; Sagoe, Kwamena W. C.; Promwong, Charupon; Permpikul, Parichart; Fongsatitkul, Ladda; Glynn, Diarmuid M.; Sibinga, Cees T. Smit; Postma, Maarten J.
BACKGROUND: The goal of our research was to actively involve decision makers in the economic assessment of screening strategies in their region. This study attempted to accomplish this by providing an easy-to-use Web interface at http://www.bloodsafety.info that allows decision makers to adapt this
The new interface of the Web of Science (Thomson Reuters) enables users to retrieve sets larger than 100,000 documents in a single search. This makes it possible to compare publication trends for China, the USA, EU-27, and smaller countries with the data in the Scopus (Elsevier) database. China no l
L Jegatha Deborah; R Sathiyaseelan; S Audithan; P Vijayakumar
he e-learners' excellence can be improved by recommending suitable e-contents available in e-learning servers that are based on investigating their learning styles. The learning styles had to be predicted carefully, because the psychological balance is variable in nature and the e-learners are diversified based on the learning patterns, environment, time and their mood. Moreover, the knowledge about the learners used for learning style prediction is uncertain in nature. This paper identifies Felder–Silverman learning style model as a suitable model for learning style prediction, especially in web environments and proposes to use Fuzzy rules to handle the uncertainty in the learning style predictions. The evaluations have used the Gaussian membership function based fuzzy logic for 120 students and tested for learning of C programming language and it has been observed that the proposed model improved the accuracy in prediction significantly.
Martinez, Alicia; Estrada, Hugo; Molina, Alejandra; Mejia, Manuel; Perez, Joaquin
The mechanisms to communicate emotions have dramatically changed in the last 10 years with social networks, where users massively communicate their emotional states by using the Internet. However, people with socialization problems have difficulty expressing their emotions verbally or interpreting the environment and providing an appropriate emotional response. In this paper, a novel solution called the Emotion-Bracelet is presented that combines a hardware device and a software system. The proposed approach identifies the polarity and emotional intensity of texts published on a social network site by performing real-time processing using a web service. It also shows emotions with a LED matrix using five emoticons that represent positive, very positive, negative, very negative, and neutral states. The Emotion-Bracelet is designed to help people express their emotions in a non-intrusive way, thereby expanding the social aspect of human emotions. PMID:27886130
Full Text Available Information and communication technology plays essential role for people’s day-to-day business activities. People receive most of their knowledge by processing, recording and transferring necessary information through surfing Internet websites. Internet as an essential part of information technology (IT has grown remarkably. Nowadays, there have been significant amount of efforts in Iran for developing e-commerce. This paper studies the effects of environmental internet features on internet purchase intention. The study divides internet environment into demographic and technologic parts and, for studying each of them, many features are investigated such as internet connection speed, connectivity model, web browser, type of payments, user’s income, user’s education, user’s gender, frequency of online usage per week and users’ goal for using internet. Using Logistic regression technique, the study has determined a meaningful effects of income, education, connection type, browser and goal on consumers’ behavior.
macroscopic conservation equations with an order parameter which can account for the solid, liquid, and the mushy zones with the help of a phase function defined on the basis of the liquid fraction, the Gibbs relation, and the phase diagram with local approximations. Using the above formalism for alloy solidification, the width of the diffuse interface (mushy zone was computed rather accurately for iron-carbon and ammonium chloride-water binary alloys and validated against experimental data from literature.
Full Text Available Abstract This paper covers the use of depth sensors such as Microsoft Kinect and ASUS Xtion to provide a natural user interface (NUI for controlling 3-D (three-dimensional virtual globes such as Google Earth (including its Street View mode, Bing Maps 3D, and NASA World Wind. The paper introduces the Microsoft Kinect device, briefly describing how it works (the underlying technology by PrimeSense, as well as its market uptake and application potential beyond its original intended purpose as a home entertainment and video game controller. The different software drivers available for connecting the Kinect device to a PC (Personal Computer are also covered, and their comparative pros and cons briefly discussed. We survey a number of approaches and application examples for controlling 3-D virtual globes using the Kinect sensor, then describe Kinoogle, a Kinect interface for natural interaction with Google Earth, developed by students at Texas A&M University. Readers interested in trying out the application on their own hardware can download a Zip archive (included with the manuscript as additional files 1, 2, &3 that contains a 'Kinnogle installation package for Windows PCs'. Finally, we discuss some usability aspects of Kinoogle and similar NUIs for controlling 3-D virtual globes (including possible future improvements, and propose a number of unique, practical 'use scenarios' where such NUIs could prove useful in navigating a 3-D virtual globe, compared to conventional mouse/3-D mouse and keyboard-based interfaces. Additional file 1 Installation package for Kinoogle (part 1 of 3. Compressed (zipped archive containing Kinoogle's installation package for Microsoft Windows operating systems. Download and unzip the contents of Additional file 1, Additional file 2, and Additional file 3 to the same hard drive location, then run 'Additional_file.part1.exe' from that location. Click here for file Additional file 2 Installation package for Kinoogle (part 2
The Hidden Web databases contain much more searchable information than the Surface Web databases. If the query interfaces on the Deep Web are integrated, the recall and precision of web information retrieval will be highly improved. This paper discusses the clustering analysis for query schema integration problem. The query＇ interface schema integration method costs less, compared with the Deep Web data source integration.%Deep Web信息是隐藏在Web服务器中可搜索的数据库信息资源，其信息量远比表面web信息量大。将Deep Web信息查询的接口模式集成为统一的查询接口，将极大地提高web信息检索的查全率和查准率。讨论了查询模式集成问题的聚类分析方法，相对于直接对Deep Web数据源的进行集成，对查询模式加以集成的思路成本更低。
Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca
Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407
Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca
Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.
Schaefer, R. K.; Paxton, L. J.; Romeo, G.; Wolven, B. C.; Zhang, Y.; Comberiate, J.
With it's high inclination orbit, GUVI provides global coverage of the ionosphere/thermosphere system, revisiting each polar region 15 times a day. The GUVI instrument has long been a resource for the ITM community with a panoply of data products available from the GUVI website (http://guvi.jhuapl.edu). GUVI is in a high inclination orbit and so provides coverage of both hemispheres. With the release last year of the data products from the DMSO/SSUSI instrument, particularly more detailed auroral zone products (Q, E0, Hemispheric Power, discrete auroral arcs, proton precipitation regions), new equatorial ionospheric products (3D electron densities, bubbles), a whole new set of UV data products has become available. SSUSI are available from http://ssusi.jhuapl.edu. To leverage the experience and knowledge gained from running all of these instruments we have adapted the SSUSI products so they can be made from GUVI telemetry. There are now updated versions of GUVI legacy products as well as brand new products. In addition, better on-orbit calibration techniques developed for SSUSI have now been applied to the GUVI instrument calibration - there is now a common set of software for calibrating both instruments. With a common data format, calibration, and product definition, the data from all SSUSI and GUVI instruments can now be easily combined to get multiple instruments to cover the hemispheres to do a variety of global studies. In addition, the GUVI spectrographic mode data provides great detail about spectrographic features (e.g. O/N2 ratios, NO band emission) that are important for understanding dynamical processes in the thermosphere. A new version of the GUVI website (with the same interface as the SSUSI website) has been launched from guvi.jhuapl.edu to showcase the legacy products made with the new calibration and also highlight the newly developed products for the GUVI imaging and spectrographic modes.
Soh, Jung; Dong, Xiaoli; Caffrey, Sean M; Voordouw, Gerrit; Sensen, Christoph W
We have developed Phoenix 2, a ribosomal RNA gene sequence analysis pipeline, which can be used to process large-scale datasets consisting of more than one hundred environmental samples and containing more than one million reads collectively. Rapid handling of large datasets is made possible by the removal of redundant sequences, pre-partitioning of sequences, parallelized clustering per partition, and subsequent merging of clusters. To build the pipeline, we have used a combination of open-source software tools and custom-developed Perl scripts. For our project we utilize hardware-accelerated searches, but it is possible to reconfigure the analysis pipeline for use with generic computing infrastructure only, with a considerable reduction in speed. The set of analysis results produced by Phoenix 2 is comprehensive, including taxonomic annotations using multiple methods, alpha diversity indices, beta diversity measurements, and a number of visualizations. To date, the pipeline has been used to analyze more than 1500 environmental samples from a wide variety of microbial communities, which are part of our Hydrocarbon Metagenomics Project (http://www.hydrocarbonmetagenomics.com). The software package can be installed as a local software suite with a Web interface. Phoenix 2 is freely available from http://sourceforge.net/projects/phoenix2.
Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.
FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are
Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints
MATLAB图形用户界面环境(GUIDE)一直都无法实现类似VC窗体滚动条的功能.介绍了一种在MATLAB GUIDE中使用WebBrowser控件,利用网页自动生成滚动条的特性,实现大量内容显示的方法.并着重介绍了WebBrowser控件的创建,按钮、文本、图像的添加与显示,以及MATLAB与WebBrowser控件数据传递的方法.通过图像分类系统对此方法进行验证,表明该方法在MATLAB图形用户界面(GUI)设计中具有简单、易扩展的特性.%MATLAB graphical user interfaces development environment (GUIDE) has been unable to achieve the function of scroll bar based on the VC form.This paper introduces a method of displaying large amounts of content that using a WebBrowser ActiveX in MATLAB GUIDE, and utilizes the characteristics of scroll bar's automatic generation in web page to achieve an abundant displaying result.This essay mainly focuses on the creation of WebBrowser controls, adding and displaying the buttons, texts, images in WebBrowser ActiveX, and data transfers between MATLAB and web controls.This method is validated through image classification system, since the results demonstrate its simplicity and expansibility.
Goble, Carole; Stevens, Robert
Data integration is a perennial issue in bioinformatics, with many systems being developed and many technologies offered as a panacea for its resolution. The fact that it is still a problem indicates a persistence of underlying issues. Progress has been made, but we should ask "what lessons have been learnt?", and "what still needs to be done?" Semantic Web and Web 2.0 technologies are the latest to find traction within bioinformatics data integration. Now we can ask whether the Semantic Web, mashups, or their combination, have the potential to help. This paper is based on the opening invited talk by Carole Goble given at the Health Care and Life Sciences Data Integration for the Semantic Web Workshop collocated with WWW2007. The paper expands on that talk. We attempt to place some perspective on past efforts, highlight the reasons for success and failure, and indicate some pointers to the future.
Johnson, Kathy A.
For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.
In bioinformatics, there are often a large number of input features. For example, there are millions of single nucleotide polymorphisms (SNPs) that are genetic variations which determine the dierence between any two unrelated individuals. In microarrays, thousands of genes can be proled in each test. It is important to nd out which input features (e.g., SNPs or genes) are useful in classication of a certain group of people or diagnosis of a given disease. In this paper, we investigate some powerful feature selection techniques and apply them to problems in bioinformatics. We are able to identify a very small number of input features sucient for tasks at hand and we demonstrate this with some real-world data.
This paper provides an overview of methods and current applications of distributed computing in bioinformatics. Distributed computing is a strategy of dividing a large workload among multiple computers to reduce processing time, or to make use of resources such as programs and databases that are not available on all computers. Participating computers may be connected either through a local high-speed network or through the Internet.
Bhagat, Jiten; Tanoh, Franck; Nzuobontane, Eric; Laurent, Thomas; Orlowski, Jerzy; Roos, Marco; Wolstencroft, Katy; Aleksejevs, Sergejs; Stevens, Robert; Pettifer, Steve; Lopez, Rodrigo; Goble, Carole A
The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable 'Web 2.0'-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.
Glez-Peña, Daniel; Lourenço, Anália; López-Fernández, Hugo; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino
Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applic...
Burr, Tom L [Los Alamos National Laboratory
Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.
Full Text Available Abstract Background The creation of successful health policy and location of resources increasingly relies on evidence-based decision-making. The development of intuitive, accessible tools to analyse, display and disseminate spatial data potentially provides the basis for sound policy and resource allocation decisions. As health services are rationalized, the development of tools such graphical user interfaces (GUIs is especially valuable at they assist decision makers in allocating resources such that the maximum number of people are served. GIS can used to develop GUIs that enable spatial decision making. Results We have created a Web-based GUI (wGUI to assist health policy makers and administrators in the Canadian province of British Columbia make well-informed decisions about the location and allocation of time-sensitive service capacities in rural regions of the province. This tool integrates datasets for existing hospitals and services, regional populations and road networks to allow users to ascertain the percentage of population in any given service catchment who are served by a specific health service, or baskets of linked services. The wGUI allows policy makers to map trauma and obstetric services against rural populations within pre-specified travel distances, illustrating service capacity by region. Conclusion The wGUI can be used by health policy makers and administrators with little or no formal GIS training to visualize multiple health resource allocation scenarios. The GUI is poised to become a critical decision-making tool especially as evidence is increasingly required for distribution of health services.
Gelbart, Hadas; Yarden, Anat
Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…
McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo
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.
displayed using the one - click standard web practice of text that is blue underlined initially and turns purple underlined after the link is followed. The...listed, the hover-over field may indicate ’ATIS link’. To view figures, foldouts, or tables, when not in-line, use one click standard web practice of... one click . Links to view animations, videos, etc. should use one - click standard web practices of text that is blue underlined initially and turns
de Groot Joost CW
Full Text Available Abstract Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible. Results We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1 a web based, graphical user interface (GUI that enables a pipeline operator to manage the system; 2 the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3 the Executor, which searches for scheduled jobs and executes these on a compute cluster. Conclusion The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.
Yarfitz, S; Ketchell, D S
Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries. The University of Washington Health Sciences Libraries have been providing specialized services to this user community since 1995. The library recruited a Ph.D. biologist to assess the molecular biological information needs of researchers and design strategies to enhance library resources and services. A survey of laboratory research groups identified areas of greatest need and led to the development of a three-pronged program: consultation, education, and resource development. Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site. Bioinformatics clients are drawn from diverse departments and include clinical researchers in need of tools that are not readily available outside of basic sciences laboratories. Evaluation and usage statistics indicate that researchers, regardless of departmental affiliation or position, require support to access molecular biology and genetics resources. Centralizing such services in the library is a natural synergy of interests and enhances the provision of traditional library resources. Successful implementation of a library-based bioinformatics program requires both subject-specific and library and information technology expertise.
Yarfitz, Stuart; Ketchell, Debra S.
Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries. The University of Washington Health Sciences Libraries have been providing specialized services to this user community since 1995. The library recruited a Ph.D. biologist to assess the molecular biological information needs of researchers and design strategies to enhance library resources and services. A survey of laboratory research groups identified areas of greatest need and led to the development of a three-pronged program: consultation, education, and resource development. Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site. Bioinformatics clients are drawn from diverse departments and include clinical researchers in need of tools that are not readily available outside of basic sciences laboratories. Evaluation and usage statistics indicate that researchers, regardless of departmental affiliation or position, require support to access molecular biology and genetics resources. Centralizing such services in the library is a natural synergy of interests and enhances the provision of traditional library resources. Successful implementation of a library-based bioinformatics program requires both subject-specific and library and information technology expertise. PMID:10658962
de Ridder, Dick; de Ridder, Jeroen; Reinders, Marcel J T
Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained.
Full Text Available Illiterate and semi-literate people usually face different types of difficulties when they use the Internet, such as reading and recognising text. This research aims to develop and examine the influence of adopting a text-free user interface on the usability of a web-based government system with illiterate and semi-literate people. A number of steps have been followed in order to achieve this research goal. An extensive literature review has been carried out to explore the adoption of different concepts or representations of content to help illiterate/semi-literate people in Information and Communication Technology (ICT projects. Then a consolidated framework is proposed and adopted in order to develop a text-free user interface. This can help in building a text-free user interface for a certain service here in Saudi Arabia. Cultural factors, education level, text-free icons, and usability guidelines have been considered in the above-mentioned framework. A prototype of a web-based government system after taking into account the above framework has been designed and developed. Usability testing and heuristic evaluation have been used as usability assessment methods in order to evaluate the system usability and its impact on the usability for illiterate people in Saudi Arabia. The results are encouraging as the achieved results of usability measures imply that adopting the consolidated framework has influenced the usability in this research.
Blaz, Jacquelyn W; Pearce, Patricia F
The world is becoming increasingly web-based. Health care institutions are utilizing the web for personal health records, surveillance, communication, and education; health care researchers are finding value in using the web for research subject recruitment, data collection, and follow-up. Programming languages, such as Java, require knowledge and experience usually found only in software engineers and consultants. The purpose of this paper is to demonstrate Ruby on Rails as a feasible alternative for programming questionnaires for use on the web. Ruby on Rails was specifically designed for the development, deployment, and maintenance of database-backed web applications. It is flexible, customizable, and easy to learn. With a relatively little initial training, a novice programmer can create a robust web application in a small amount of time, without the need of a software consultant. The translation of the Children's Computerized Physical Activity Reporter (C-CPAR) from a local installation in Microsoft Access to a web-based format utilizing Ruby on Rails is given as an example.
Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W
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.
李晓; 王雪飞; 邱玉辉
An adaptive user interface helps to improve the quality of human-computer interaction. Most people at present join to Web-Based Learning by common browser. Due to the one-fits-all user interface, they have to face with the problem of lack of the support on personalized learning. The design and implementation of the adaptive user interface for Web-based learning in this paper is grounded in our work done before, for example interaction model,adaptive user models including domain models. The adaptivity is mainly expressed on learning contents and representation including layout as well as operation.
Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan
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.
Tolvanen, Martti; Vihinen, Mauno
Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…
Vitevitch, Michael S; Stamer, Melissa K; Kieweg, Douglas
A number of resources provide psycholinguistic researchers with information about the words that the typical child or adult knows in a variety of languages. What is currently not available is a resource that provides information about the words that a typical adult learning a foreign language knows. We created such a resource for Spanish: The Beginning Spanish Lexicon. The present report describes the words contained in this web-accessible resource, and the information about those words provided by the interface. This information is freely accessible at: http://www.people.ku.edu/~mvitevit/BegSpanLex.html.
Cantacessi, C; Campbell, B E; Jex, A R; Young, N D; Hall, R S; Ranganathan, S; Gasser, R B
The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention.
Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...
@@ With the completion of human genome sequencing, a new era of bioinformatics st arts. On one hand, due to the advance of high throughput DNA microarray technol ogies, functional genomics such as gene expression information has increased exp onentially and will continue to do so for the foreseeable future. Conventional m eans of storing, analysing and comparing related data are already overburdened. Moreover, the rich information in genes , their functions and their associated wide biological implication requires new technologies of analysing data that employ sophisticated statistical and machine learning algorithms, powerful com puters and intensive interaction together different data sources such as seque nce data, gene expression data, proteomics data and metabolic pathway informati on to discover complex genomic structures and functional patterns with other bi ological process to gain a comprehensive understanding of cell physiology.
Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.
Baier, Rosa R.; Cooper, Emily; Wysocki, Andrea; Gravenstein, Stefan; Clark, Melissa
Introduction: 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. Methods: Healthcentric Advisors and Brown University undertook a multi-phased approach to create a consumer-facing home health web application in Rhode Island. This included reviewi...
Tolvanen, Martti; Vihinen, Mauno
Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material over the Internet. Currently, we provide two fully computer-based courses, "Introduction to Bioinformatics" and "Bioinformatics in Functional Genomics." Here we will discuss the application of distance learning in bioinformatics training and our experiences gained during the 3 years that we have run the courses, with about 400 students from a number of universities. The courses are available at bioinf.uta.fi.
Full Text Available Abstract Background The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client – Gbrowse Moby – that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. Results Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. Conclusion Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment.
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.
Lawlor, Brendan; Walsh, Paul
There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.
Bushell Michael E
Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a
de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.
Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.
DR. ANURADHA; BABITA AHUJA
In this era of digital tsunami of information on the web, everyone is completely dependent on the WWW for information retrieval. This has posed a challenging problem in extracting relevant data. Traditional web crawlers focus only on the surface web while the deep web keeps expanding behind the scene. The web databases are hidden behind the query interfaces. In this paper, we propose a Hidden Web Extractor (HWE) that can automatically discover and download data from the Hidden Web databases. ...
Muhammad Ali Masood
Full Text Available Dealing with data means to group information into a set of categories either in order to learn new artifacts or understand new domains. For this purpose researchers have always looked for the hidden patterns in data that can be defined and compared with other known notions based on the similarity or dissimilarity of their attributes according to well-defined rules. Data mining, having the tools of data classification and data clustering, is one of the most powerful techniques to deal with data in such a manner that it can help researchers identify the required information. As a step forward to address this challenge, experts have utilized clustering techniques as a mean of exploring hidden structure and patterns in underlying data. Improved stability, robustness and accuracy of unsupervised data classification in many fields including pattern recognition, machine learning, information retrieval, image analysis and bioinformatics, clustering has proven itself as a reliable tool. To identify the clusters in datasets algorithm are utilized to partition data set into several groups based on the similarity within a group. There is no specific clustering algorithm, but various algorithms are utilized based on domain of data that constitutes a cluster and the level of efficiency required. Clustering techniques are categorized based upon different approaches. This paper is a survey of few clustering techniques out of many in data mining. For the purpose five of the most common clustering techniques out of many have been discussed. The clustering techniques which have been surveyed are: K-medoids, K-means, Fuzzy C-means, Density-Based Spatial Clustering of Applications with Noise (DBSCAN and Self-Organizing Map (SOM clustering.
WWW(World Wide Web)系统和数据库是网络化信息服务的基础.通过对Web和数据库方面的主要技术(包括标准CGI,ISAPI,JDBC,IDC,ASP技术)进行详细论述,就基于IIS实现WWW与数据库互联的实际应用作了具体描述.
石龙; 强保华; 何倩; 吴春明; 谌超
Query interface schema extraction is the precondition of Deep Web data integration. Generally query interface schema consists of a set of domain-related attributes, and one attribute is formed by a single element or a combination of multi-elements. The current researches on attribute extraction are mostly based on the single element fashion, and those multi-elements based are few. Aiming at the case of multi-elements attribute extraction, a DOM-based method for query interface schema extraction is proposed. This method parses query interface to become a DOM and extracts the form elements base on the corresponding DOM nodes. The method employs two-phase clustering algorithms to cluster the form elements, mines the combination relationship of them and combines elements to realize attributes extraction. This method has a favorable performance at both single-element and multi-elements attribute extraction. The experimental result shows that this method is effective.%属性抽取主要基于单元素属性抽取,而多元素属性抽取的研究较少.针对多元素组成属性情况进行研究,提出一种基于查询接口DOM结构的属性抽取方法,该方法将查询接口解析成DOM,基于DOM节点提取查询接口上对应的表单元素,对从查询接口上提取获得的元素集合进行二次聚类,挖掘元素之间的组合关系,最终将元素组合形成属性.这种方法能很好地抽取接口上的单元素属性和多元素属性,实验结果表明了方法的有效性.
The new interface of the Web of Science (of Thomson Reuters) enables users to retrieve sets larger than 100,000 documents in a single search. This makes it possible to compare publication trends for China, the USA, EU-27, and a number of smaller countries. China no longer grew exponentially during the 2000s, but linearly. Contrary to previous predictions on the basis of exponential growth or Scopus data, the cross-over of the lines for China and the USA is postponed to the next decade (after 2020) according to this data. These extrapolations, however, should be used only as indicators and not as predictions. Along with the dynamics in the publication trends, one also has to take into account the dynamics of the databases used for the measurement.
胡聪; 高明; 牛军浩
LXI is applied and extended the technology of Ethernet in field of auto - testing. For popularizing the new network standard, the feature points and its key technic of LXI are studied) The NORCO - 3680ALE as embedded motherboard and PM512B as a function circuit were adopted as the LXI bus interface hardware; The configuration and application of Web server mini httpd based on the Linux operating system, CSP Program Design, Ajax technology and the Makefile configuration and generation of CGI program were highlighted; Finally to measure voltage by remote accessing CGI programs through browser. The test results show that the system can implement voltage measurement correctly, achieve instrument control of Web interface and conform to the LXI standard.%LXI是以太网技术在测试自动化领域的应用和拓展;为了将LXI这一新型网络标准更广泛的推广和应用,研究了LXI的特征及其技术要点;构建了以NORCO-3680ALE为嵌入式主板、以PM512B为功能电路的LXI总线接口的硬件;重点阐述了基于Linux操作系统的Web服务器min_httpd的配置及应用,CSP程序的设计,Ajax技术的应用和CGI程序Makefile的配置及生成;最后经浏览器远程访问CGI程序,进行电压测量;试验结果表明,系统能正确地进行电压测量,实现了Web接口的仪器控制,符合LXI标准.
With the rapid expansion and development of Internet and WWW (World Wide Web or Web), Web GIS (Web Geographical Information Systen) is becoming ever more popular and as a result numerous sites have added GIS capability on their Web sites. In this paper, the reasons behind developing a Web GIS instead of a “traditional” GIS are first outlined. Then the current status of Web GIS is reviewed, and their implementation methodologies are explored as well.The underlying technologies for developing Web GIS, such as Web Server, Web browser, CGI (Common Gateway Interface), Java, ActiveX, are discussed, and some typical implementation tools from both commercial and public domain are given as well. Finally, the future development direction of Web GIS is predicted.
元书俊; 朱守中; 金灵芝
deep web 数据源中的信息可以通过查询提交进行访问,因此分析一个查询接口的查询能力是非常关键的,本文基于原子查询的理念,提出了一种通过识别查询接口上所有原子查询的方法来估计deep web接口查询能力.
Placidi, Giuseppe; Petracca, Andrea; Spezialetti, Matteo; Iacoviello, Daniela
A Brain Computer Interface (BCI) allows communication for impaired people unable to express their intention with common channels. Electroencephalography (EEG) represents an effective tool to allow the implementation of a BCI. The present paper describes a modular framework for the implementation of the graphic interface for binary BCIs based on the selection of symbols in a table. The proposed system is also designed to reduce the time required for writing text. This is made by including a motivational tool, necessary to improve the quality of the collected signals, and by containing a predictive module based on the frequency of occurrence of letters in a language, and of words in a dictionary. The proposed framework is described in a top-down approach through its modules: signal acquisition, analysis, classification, communication, visualization, and predictive engine. The framework, being modular, can be easily modified to personalize the graphic interface to the needs of the subject who has to use the BCI and it can be integrated with different classification strategies, communication paradigms, and dictionaries/languages. The implementation of a scenario and some experimental results on healthy subjects are also reported and discussed: the modules of the proposed scenario can be used as a starting point for further developments, and application on severely disabled people under the guide of specialized personnel.
Stevens, R; Miller, C
Bioinformaticians seeking to provide services to working biologists are faced with the twin problems of distribution and diversity of resources. Bioinformatics databases are distributed around the world and exist in many kinds of storage forms, platforms and access paradigms. To provide adequate services to biologists, these distributed and diverse resources have to interoperate seamlessly within single applications. The Common Object Request Broker Architecture (CORBA) offers one technical solution to these problems. The key component of CORBA is its use of object orientation as an intermediate form to translate between different representations. This paper concentrates on an explanation of object orientation and how it can be used to overcome the problems of distribution and diversity by describing the interfaces between objects.
Based on a comparative study of Cambridge Scientific Abstracts' Internet Database Service and OCLC's FirstSearch, this paper discusses the user-friendly interfaces of Web-based databases according to their characteristics such as database selection, search strategy formulation and reformulation, online help and result output.
Wattam, Alice R.; Davis, James J.; Assaf, Rida; Boisvert, Sébastien; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Dietrich, Emily M.; Disz, Terry; Gabbard, Joseph L.; Gerdes, Svetlana; Henry, Christopher S.; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olsen, Gary J.; Murphy-Olson, Daniel E.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Warren, Andrew; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L.
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by ‘virtual integration’ to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics. PMID:27899627
Full Text Available Bioinformatics, for its very nature, is devoted to a set of targets that constantly evolve. Training is probably the best response to the constant need for the acquisition of bioinformatics skills. It is interesting to assess the effects of training in the different sets of researchers that make use of it. While training bench experimentalists in the life sciences, we have observed instances of changes in their attitudes in research that, if well exploited, can have beneficial impacts in the dialogue with professional bioinformaticians and influence the conduction of the research itself.
茅琴娇; 冯博琴; 潘善亮
为了进一步提高搜索引擎的效率,实现对deep web中所蕴含的大量有用信息的检索、索引和定位,引入潜在语义分析理论是一种简单而有效的方法.通过对作为deep web站点入口的查询界面里的表单属性进行潜在语义分析,从表单属性中挖掘出潜在语义结构,并实现一定程度上的降维.利用这种潜在语义结构,推断对应站点的数据内容并改善不同站点的相似度计算.实验结果显示,潜在语义分析修正和改善了deep web站点的表单属性的语义理解,弥补了单纯的关键字匹配带来的一些不足.该方法可以被用来实现为某一站点查找网络上相似度高的站点及通过键入表单属性给出拥有相似表单的站点列表.%To further enhance the efficiencies of search engines, achieving capabilities of searching, indexing and locating the information in the deep web, latent semantic analysis is a simple and effective way. Through the latent semantic analysis of the attributes in the query interfaces and the unique entrances of the deep web sites, the hidden semantic structure information can be retrieved and dimension reduction can be achieved to a certain extent. Using this semantic structure information, the contents in the site can be inferred and the similarity measures among sites in deep web can be revised. Experimental results show that latent semantic analysis revises and improves the semantic understanding of the query form in the deep web, which overcomes the shortcomings of the keyword-based methods. This approach can be used to effectively search the most similar site for any given site and to obtain a site list which conforms to the restrictions one specifies.
Palmer, L E; O'Shaughnessy, A L; Preston, R R; Santos, L; Balija, V S; Nascimento, L U; Zutavern, T L; Henthorn, P S; Hannon, G J; McCombie, W R
We have initially sequenced approximately 8,000 canine expressed sequence tags (ESTs) from several complementary DNA (cDNA) libraries: testes, whole brain, and Madin-Darby canine kidney (MDCK) cells. Analysis of these sequences shows that they provide partial sequence information for about 5%-10% of the canine genes. An analysis pipeline has been created to cluster the ESTs and to map individual ESTs as well as clustered ESTs to both the human genome and the human proteome. Gene ontology (GO) terms have been assigned to the ESTs and clusters based on their top matches to the International Protein Index (IPI) set of human proteins. The data generated is stored in a MySQL relational database for analysis and display. A Web-based Perl script has been written to display the analyzed data to the scientific community.
Meganck, B.; Mergen, P.; Meirte, D.
The following text presents some personal ideas about the way (bio)informatics2 is heading, along with some examples of how our institution – the Royal Museum for Central Africa (RMCA) – is gearing up for these new times ahead. It tries to find the important trends amongst the buzzwords, and to demo
Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael
Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…
Elwess, Nancy L.; Latourelle, Sandra M.; Cauthorn, Olivia
One of the hottest areas of science today is the field in which biology, information technology,and computer science are merged into a single discipline called bioinformatics. This field enables the discovery and analysis of biological data, including nucleotide and amino acid sequences that are easily accessed through the use of computers. As…
This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...
The Virginia Bioinformatics Institute at Virginia Tech, in collaboration with Virginia Tech's Ph.D. program in genetics, bioinformatics, and computational biology, has awarded three fellowships in support of graduate work in transdisciplinary team science.
Full Text Available Abstract 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.
Recently, a new web development technique for creating interactive web applications, dubbed AJAX, has emerged in response to the limited degree of interactivity in large-grain stateless web interactions. In this new model, the web interface is composed of individual components which can be updated/r
By anglicizing the limitations of existing evidence theory method for Deep Web interface integration, a Deep Web pattern matching method based on concept word and semantic heterogeneity model is proposed. The method preprocesses pattern through extracting concept word, discriminates and combines group attributes to convert m: n complex matching into 1 : 1 simple matching for improving implement efficiency. By introducing instance into semantic heterogeneity model, the problem of mining semantic heterogeneity synonymy attributes is resolved by computing, synthetic evaluating, and selecting similarity values of attribute features. Experimental results indicate that compared with evidence theory method, the efficiency and accuracy of the method is improved obviously.%针对已有证据理论(DS)方法在深层网接口集成方面的局限性,设计一种基于概念词与语义异构模型的深层网模式匹配方法.通过提取概念词对概念词模型进行预处理,识别并组合成组属性,使m∶n的复杂匹配转变为1∶1的简单匹配,提高系统执行速度.在语义异构模型中引入属性实例,将挖掘语义异构的同义属性问题,转化为对属性间各特征相似值的计算、综合评测和选取问题.实验结果表明,该方法在匹配效率和准确率上较DS方法有较大改进.
Bioinformatics is a usage of information technology to help solve biological problems by designing novel and in-cisive algorithms and methods of analyses.Bioinformatics becomes a discipline vital in the era of post-genom-ics.In this review article,the application of bioinformatics in tropical medicine will be presented and dis-cussed.
李雪玲; 施化吉; 兰均; 李星毅
针对现有Deep Web查询接口判定方法误判较多、无法有效区分搜索引擎类接口的不足,提出了基于决策树和链接相似的Deep Web查询接口判定方法.该方法利用信息增益率选取重要属性,并构建决策树对接口表单进行预判定,识别特征较为明显的接口;然后利用基于链接相似的判定方法对未识别出的接口进行二次判定,准确识别真正查询接口,排除搜索引擎类接口.结果表明,该方法能有效区分搜索引擎类接口,提高了分类的准确率和查全率.%In order to solve the problems existed in the traditional method that Deep Web query interfaces are more false positives and search engine class interface can not be effectively distinguished, this paper proposed a Deep Web query interface identification method based on decision tree and link-similar. This method used attribute information gain ratio as selection level, built a decision tree to pre-determine the form of the interfaces to identify the most interfaces which had some distinct features, and then used a new method based on link-similar to identify these unidentified again, distinguishing between Deep Web query interface and the interface of search engines. The result of experiment shows that it can enhance the accuracy and proves that it is better than the traditional methods.
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.
Verheggen, Kenneth; Maddelein, Davy; Hulstaert, Niels; Martens, Lennart; Barsnes, Harald; Vaudel, Marc
The use of proteomics bioinformatics substantially contributes to an improved understanding of proteomes, but this novel and in-depth knowledge comes at the cost of increased computational complexity. Parallelization across multiple computers, a strategy termed distributed computing, can be used to handle this increased complexity; however, setting up and maintaining a distributed computing infrastructure requires resources and skills that are not readily available to most research groups. Here we propose a free and open-source framework named Pladipus that greatly facilitates the establishment of distributed computing networks for proteomics bioinformatics tools. Pladipus is straightforward to install and operate thanks to its user-friendly graphical interface, allowing complex bioinformatics tasks to be run easily on a network instead of a single computer. As a result, any researcher can benefit from the increased computational efficiency provided by distributed computing, hence empowering them to tackle more complex bioinformatics challenges. Notably, it enables any research group to perform large-scale reprocessing of publicly available proteomics data, thus supporting the scientific community in mining these data for novel discoveries.
With the development of power industry , it is hoped that the power industry marketing and acquisition can become an integrated information platform in order to provide a unified management , and realize data sharing among systems.This paper in-troduces a way of power marketing and acquisition data exchange under heterogeneous circumstance .Taking a county power ac-quisition data uploaded to the provincial center as a case , it is proved that this scheme can realize the interface of power market-ing and acquisition services.% 随着电力行业的发展，电力行业的营销和采集希望整合成一体化的信息平台，提供统一管理，实现系统之间的数据共享。基于Web Service提出一种异构环境下电力营销与采集数据交换方法，以某县电力采集数据上传到省中心为实例，进行实例实践，实际应用表明，该方案可以实现电力营销与采集业务。
Schweighofer, Karl; Pohorille, Andrew
Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.
Jones, Andrew R; Hubbard, Simon J
This book is part of the Methods in Molecular Biology series, and provides a general overview of computational approaches used in proteome research. In this chapter, we give an overview of the scope of the book in terms of current proteomics experimental techniques and the reasons why computational approaches are needed. We then give a summary of each chapter, which together provide a picture of the state of the art in proteome bioinformatics research.
Antonio d'Acierno; Angelo Facchiano; Anna Marabotti
We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type Ⅰ. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.
Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.
Holtzclaw, J. David; Eisen, Arri; Whitney, Erika M.; Penumetcha, Meera; Hoey, J. Joseph; Kimbro, K. Sean
Many students at minority-serving institutions are underexposed to Internet resources such as the human genome project, PubMed, NCBI databases, and other Web-based technologies because of a lack of financial resources. To change this, we designed and implemented a new bioinformatics component to supplement the undergraduate Genetics course at…
Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response...... and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review...
Despite all of the UI toolkits available today, it's still not easy to design good application interfaces. This bestselling book is one of the few reliable sources to help you navigate through the maze of design options. By capturing UI best practices and reusable ideas as design patterns, Designing Interfaces provides solutions to common design problems that you can tailor to the situation at hand. This updated edition includes patterns for mobile apps and social media, as well as web applications and desktop software. Each pattern contains full-color examples and practical design advice th
Full Text Available In this era of digital tsunami of information on the web, everyone is completely dependent on the WWW for information retrieval. This has posed a challenging problem in extracting relevant data. Traditional web crawlers focus only on the surface web while the deep web keeps expanding behind the scene. The web databases are hidden behind the query interfaces. In this paper, we propose a Hidden Web Extractor (HWE that can automatically discover and download data from the Hidden Web databases. Since the only “entry point” to a Hidden Web site is a query interface, the main challenge that a Hidden WebExtractor has to face is how to automatically generate meaningful queries for the unlimited number of website pages.
Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.
Carrillo-Tripp, Mauricio; Shepherd, Craig M; Borelli, Ian A; Venkataraman, Sangita; Lander, Gabriel; Natarajan, Padmaja; Johnson, John E; Brooks, Charles L; Reddy, Vijay S
VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
US Agency for International Development — QWICR is a secure, online Title II commodity reporting system accessible to USAID Missions, PVO Cooperating Sponsors and Food for Peace Officers. QWICR provides PVO...
Carlisle, W. H.
This reports on a project to extend the capabilities of a Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1995 Summer Faculty Fellowship program and involved the development of a prototype component of the VRC - a database system that provides data creation and access services within a room of the VRC. In support of VRC development, NASA has assembled a laboratory containing the variety of equipment expected to be used by scientists within the VRC. This laboratory consists of the major hardware platforms, SUN, Intel, and Motorola processors and their most common operating systems UNIX, Windows NT, Windows for Workgroups, and Macintosh. The SPARC 20 runs SUN Solaris 2.4, an Intel Pentium runs Windows NT and is installed on a different network from the other machines in the laboratory, a Pentium PC runs Windows for Workgroups, two Intel 386 machines run Windows 3.1, and finally, a PowerMacintosh and a Macintosh IIsi run MacOS.
Ku, David Tawei; Chang, Chia-Chi
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…
Web Dynpro ABAP, a NetWeaver web application user interface tool from SAP, enables web programming connected to SAP Systems. The authors' main focus was to create a book based on their own practical experience. Each chapter includes examples which lead through the content step-by-step and enable the reader to gradually explore and grasp the Web Dynpro ABAP process. The authors explain in particular how to design Web Dynpro components, the data binding and interface methods, and the view controller methods. They also describe the other SAP NetWeaver Elements (ABAP Dictionary, Authorization) and
Heyer, Laurie J.
This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…
This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…
Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.
Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian
so with no computational specialist. Here we present a setup for analysis and publication of genome data of 70 species of Aspergillus fungi. The platform is based on R, Python and uses the RShiny framework to create interactive web‐applications. It allows all participants to create interactive...... analysis which can be shared with the team and in connection with publications. We present analysis for investigation of genetic diversity, secondary and primary metabolism and general data overview. The platform, the Aspergillus Mine, is a collection of analysis tools based on data from collaboration...... with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from...
石龙; 强保华; 谌超; 吴春明
With the rapid development of Internet technology,a large number of Web databases have mushroomed and the number remains in a fast-growing trend.In order to effectively organise and utilise the information which hides deeply in Web databases,it is necessary to classify and integrate them according to domains.Since the query interface of Webpage is the unique channel to access the Web database,the classification of Deep Web data source can be realised by classifying the query interfaces.In this paper,a classification method based on text VSM of query interface is proposed.The basic idea is to build a vector space model (VSM) by using query interface text information firstly.Then the typical data mining classification algorithm is employed to train one or more classifiers,thus to classify the domains the query interfaces belonging to is implemented.Experimental result shows that the approach proposed in the paper has excellent classification performance.%随着Intemet技术的快速发展,Web数据库数目庞大而且仍在快速增长.为有效组织利用深藏于Web数据库上的信息,需对其按领域进行分类和集成.Web页面上的查询接口是网络用户访问Web数据库的唯一途径,对Deep Web数据源分类可通过对查询接口分类实现.为此,提出一种基于查询接口文本VSM(Vector Space Model)的分类方法.首先,使用查询接口文本信息构建向量空间模型,然后通过典型的数据挖掘分类算法训练分类器,从而实现对查询接口所属领域进行分类.实验结果表明给出的方法具有良好的分类性能.
As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.
Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.
J.F. De Mesquita
Full Text Available In the recent years, Bioinformatics has emerged as an important research tool. Theability to mine large databases for relevant information has become essential fordifferent life science fields. On the other hand, providing education in bioinformatics toundergraduates is challenging from this multidisciplinary perspective. Therefore, it isimportant to introduced undergraduate students to the available information andcurrent methodologies in Bioinformatics. Here we report the results of a course usinga computer-assisted and problem -based learning model. The syllabus was comprisedof theoretical lectures covering different topics within bioinformatics and practicalactivities. For the latter, we developed a set of step-by-step tutorials based on casestudies. The course was applied to undergraduate students of biological andbiomedical courses. At the end of the course, the students were able to build up astep-by-step tutorial covering a bioinformatics issue.
Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.
Niriksha Bhojaraj Kabbin
Full Text Available Web applications in today’s world has a great impact on businesses and are popular since they provide business benefits and hugely deployable. Developing such efficient web applications using leading edge web technologies that promise to deliver upgraded user interface, greater scalability and interoperability, improved performance and usability, among different systems is a challenge. Google Web Toolkit (GWT is one such framework that helps to build Rich Internet Applications (RIAs that enable fertile development of high performance web applications. This paper puts an effort to provide an effective solution to develop quality web based applications with an added layer of security.
Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi
Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.
Segun A Fatumo
Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.
Pettifer, Steve; Ison, Jon; Kalas, Matús; Thorne, Dave; McDermott, Philip; Jonassen, Inge; Liaquat, Ali; Fernández, José M; Rodriguez, Jose M; Pisano, David G; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B; Bongcam-Rudloff, Erik; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K; Cameron, Graham; Vriend, Gert
The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.
Pettifer, S.; Ison, J.; Kalas, M.
The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order...... for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM......, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection...
Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T
Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.
Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong
In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.
Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.
RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....
Abstract Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environm...
Full Text Available The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4´10-4 to 2´10-2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV, between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1. Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.
Full Text Available Recent studies have demonstrated equal quality of targeted next generation sequencing (NGS compared to Sanger Sequencing. Whereas these novel sequencing processes have a validated robust performance, choice of enrichment method and different available bioinformatic software as reliable analysis tool needs to be further investigated in a diagnostic setting.DNA from 21 patients with genetic variants in SDHB, VHL, EPAS1, RET, (n=17 or clinical criteria of NF1 syndrome (n=4 were included. Targeted NGS was performed using Truseq custom amplicon enrichment sequenced on an Illumina MiSEQ instrument. Results were analysed in parallel using three different bioinformatics pipelines; (1 Commercially available MiSEQ Reporter, fully automatized and integrated software, (2 CLC Genomics Workbench, graphical interface based software, also commercially available, and ICP (3 an in-house scripted custom bioinformatic tool.A tenfold read coverage was achieved in between 95-98% of targeted bases. All workflows had alignment of reads to SDHA and NF1 pseudogenes. Compared to Sanger sequencing, variant calling revealed a sensitivity ranging from 83 to 100% and a specificity of 99.9-100%. Only MiSEQ reporter identified all pathogenic variants in both sequencing runs.We conclude that targeted next generation sequencing have equal quality compared to Sanger sequencing. Enrichment specificity and the bioinformatic performance need to be carefully assessed in a diagnostic setting. As acceptable accuracy was noted for a fully automated bioinformatic workflow, we suggest that processing of NGS data could be performed without expert bioinformatics skills utilizing already existing commercially available bioinformatics tools.
Web services are a common and standard way to implement communication between information systems and provide documented interfaces. The Web services are usually using SOAP because it is a widely-spread, well-documented and used standard. SOAP standard defines a message structure, an envelope, that is sent over internet using HTTP and contains XML data. An important part of the SOAP structure is the exception mechanism that returns a Fault element in the response. The SOAP Fault is a stan...
Healy, Marion J; Tong, Weida; Ostroff, Stephen; Eichler, Hans-Georg; Patak, Alex; Neuspiel, Margaret; Deluyker, Hubert; Slikker, William
"Regulatory Bioinformatics" strives to develop and implement a standardized and transparent bioinformatic framework to support the implementation of existing and emerging technologies in regulatory decision-making. It has great potential to improve public health through the development and use of clinically important medical products and tools to manage the safety of the food supply. However, the application of regulatory bioinformatics also poses new challenges and requires new knowledge and skill sets. In the latest Global Coalition on Regulatory Science Research (GCRSR) governed conference, Global Summit on Regulatory Science (GSRS2015), regulatory bioinformatics principles were presented with respect to global trends, initiatives and case studies. The discussion revealed that datasets, analytical tools, skills and expertise are rapidly developing, in many cases via large international collaborative consortia. It also revealed that significant research is still required to realize the potential applications of regulatory bioinformatics. While there is significant excitement in the possibilities offered by precision medicine to enhance treatments of serious and/or complex diseases, there is a clear need for further development of mechanisms to securely store, curate and share data, integrate databases, and standardized quality control and data analysis procedures. A greater understanding of the biological significance of the data is also required to fully exploit vast datasets that are becoming available. The application of bioinformatics in the microbiological risk analysis paradigm is delivering clear benefits both for the investigation of food borne pathogens and for decision making on clinically important treatments. It is recognized that regulatory bioinformatics will have many beneficial applications by ensuring high quality data, validated tools and standardized processes, which will help inform the regulatory science community of the requirements
Commercial success or failure of innovation in bioinformatics and in-silico biology requires the appropriate use of legal tools for protecting and exploiting intellectual property. These tools include patents, copyrights, trademarks, design rights, and limiting information in the form of 'trade secrets'. Potentially patentable components of bioinformatics programmes include lines of code, algorithms, data content, data structure and user interfaces. In both the US and the European Union, copyright protection is granted for software as a literary work, and most other major industrial countries have adopted similar rules. Nonetheless, the grant of software patents remains controversial and is being challenged in some countries. Current debate extends to aspects such as whether patents can claim not only the apparatus and methods but also the data signals and/or products, such as a CD-ROM, on which the programme is stored. The patentability of substances discovered using in-silico methods is a separate debate that is unlikely to be resolved in the near future.
Radhakrishnan, Sabarinathan; Tafer, Hakim; Seemann, Ernst Stefan;
, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected...... to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/....
We present SMPDF Web, a web interface for the construction of parton distribution functions (PDFs) with a minimal number of error sets needed to represent the PDF uncertainty of specific processes (SMPDF).
Full Text Available The aim of this research study is to design and implement a Wi-Fi-based control panel for remote control of lights and electrical appliances with a web functionality that allows for wide area control via the intranet or Internet. This eliminates the inconvenience of moving from one switch to another for analog operation of light fixtures and appliance in home, office and campus environment. The wireless technology we adopted is IEEE 802.11 (2008 b/g, also called Wi-Fi (Wireless Fidelity which operates in free band and is easily accessible. Wi-Ap (Wi-Fi Automated Appliance control system contains a web portal which allows for management and control purposes via the intranet or Internet. We built a standalone Wi-Ap console that allows the wireless switching on and off of any appliance(s that is(are plugged into it. The prototype we built was tested within the Electrical and Information Engineering department, Covenant University, Nigeria intranet and the test achieved our aim of remote appliances control from a web portal vial the intranet.
Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H
Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs.
Russell J. KOHEL; John Z. YU; Piyush GUPTA; Rajeev AGRAWAL
@@ There are several web sites for which information is available to the cotton research community. Most of these sites relate to resources developed or available to the research community. Few provide bioinformatic tools,which usually relate to the specific data sets and materials presented in the database. Just as the bioinformatics area is evolving, the available resources reflect this evolution.
Mandal, Chittaranjan; Sinha, Vijay Luxmi; Reade, Christopher M. P.
The architecture of a web-based course management tool that has been developed at IIT [Indian Institute of Technology], Kharagpur and which manages the submission of assignments is discussed. Both the distributed architecture used for data storage and the client-server architecture supporting the web interface are described. Further developments…
Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas
Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (" Butterfly" paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions.
Pazos, Florencio; Guijas, David; Valencia, Alfonso; De Lorenzo, Victor
Bioremediation, the exploitation of biological catalysts (mostly microorganisms) for removing pollutants from the environment, requires the integration of huge amounts of data from different sources. We have developed MetaRouter, a system for maintaining heterogeneous information related to bioremediation in a framework that allows its query, administration and mining (application of methods for extracting new knowledge). MetaRouter is an application intended for laboratories working in biodegradation and bioremediation, which need to maintain and consult public and private data, linked internally and with external databases, and to extract new information from it. Among the data-mining features is a program included for locating biodegradative pathways for chemical compounds according to a given set of constraints and requirements. The integration of biodegradation information with the corresponding protein and genome data provides a suitable framework for studying the global properties of the bioremediation network. The system can be accessed and administrated through a web interface. The full-featured system (except administration facilities) is freely available at http://pdg.cnb.uam.es/MetaRouter. Additional material: http://www.pdg.cnb.uam.es/biodeg_net/MetaRouter. PMID:15608267
Full Text Available Abstract Background The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. Results The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. Conclusions We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.
从用户角度探讨了购物网站的发展趋势、多元化界面的设计及表现,并在艾瑞咨询的基础上,从性别、年龄两方面对网站设计的影响进行了数据化的分析,指出购物网站的商品陈列规律和互动模式是体验界面的主要构成部分,阐释了界面的人性化和交互性的重要性,从而探索了新的交互界面的设计方式,强调了互动模式是未来多元化设计的基础表现。%From the user＇s angle, it discussed the development tendency diversified interface design and performance of shopping website, and based on consulting Erin, from the impact of gender, age two aspects on website design, analyzed the data and pointed out that the display rule of shopping website and interaction model was the main component of experience interface, and explained the interface of the human and the importance of interactivity, so as to explore a new way of interactive interface design, and emphasized the interaction model was the basis of future diversity design performance.
Francisco O. Martínez P.
Full Text Available Restrictions regardingnavigability and user-friendliness are the main challenges the Mobile Web faces to be accepted worldwide. W3C has recently developed the Mobile Web Initiative (MWI, a set of directives for the suitable design and presentation of mobile Web interfaces. This article presents the main features and functional modules of OneWeb, an MWI-based Web content adaptation platform developed by Mobile Devices Applications Development Interest Group’s (W@PColombia research activities, forming part of the Universidad de Cauca’s Telematics Engineering Group.Some performance measurementresults and comparison with other Web content adaptation platforms are presented. Tests have shown suitable response times for Mobile Web environments; MWI guidelines were applied to over twenty Web pages selected for testing purposes.
Reviews Equipment: BioLite Camp Stove Game: Burnout Paradise Equipment: 850 Universal interface and Capstone software Equipment: xllogger Book: Science Magic Tricks and Puzzles Equipment: Spinthariscope Equipment: DC Power Supply HY5002 Web Watch
WE RECOMMEND BioLite CampStove Robust and multifaceted stove illuminates physics concepts 850 Universal interface and Capstone software Powerful data-acquisition system offers many options for student experiments and demonstrations xllogger Obtaining results is far from an uphill struggle with this easy-to-use datalogger Science Magic Tricks and Puzzles Small but perfectly formed and inexpensive book packed with 'magic-of-science' demonstrations Spinthariscope Kit for older students to have the memorable experience of 'seeing' radioactivity WORTH A LOOK DC Power Supply HY5002 Solid and effective, but noisy and lacks portability HANDLE WITH CARE Burnout Paradise Car computer game may be quick off the mark, but goes nowhere fast when it comes to lab use WEB WATCH 'Live' tube map and free apps would be a useful addition to school physics, but maths-questions website of no more use than a textbook
Zhao, Shanrong; Lu, Jin
, including de novo library design in selection of favorable germline V gene scaffolds and CDR lengths. In addition, we have also developed a web application framework to present our knowledge database, and the web interface can help people to easily retrieve a variety of information from the knowledge database.
González-Nilo, Fernando; Pérez-Acle, Tomás; Guínez-Molinos, Sergio; Geraldo, Daniela A; Sandoval, Claudia; Yévenes, Alejandro; Santos, Leonardo S; Laurie, V Felipe; Mendoza, Hegaly; Cachau, Raúl E
After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.
Tjin-Kam-Jet, Kien-Tsoi T.E.
This proposal identifies two main problems related to deep web search, and proposes a step by step solution for each of them. The first problem is about searching deep web content by means of a simple free-text interface (with just one input field, instead of a complex interface with many input fiel
Presents a method to connect VRML (Virtual Reality Modeling Language) and Java components in a Web page using EAI (External Authoring Interface), which makes it possible to interactively generate and edit VRML meshes. The meshes used are based on regular grids, to provide an interaction and modeling
Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr
The thesis focuses on two bioinformatics research topics: the development of tools for an efficient and reliable identification of single nucleotides polymorphisms (SNPs) and polymorphic simple sequence repeats (SSRs) from expressed sequence tags (ESTs) (Chapter 2, 3 and 4), and the subsequent imple
In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…
Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...
Boyle, John A.
Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…
Kelley, Scott; Alger, Christianna; Deutschman, Douglas
The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…
Ondrej, Vladan; Dvorak, Petr
Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…
Full Text Available 2DE and 2D-DIGE based proteomics analysis of serum from women with endometriosis revealed several proteins to be dysregulated. A complete list of these proteins along with their mass spectrometry data and subsequent bioinformatics analysis are presented here. The data is related to “Investigation of serum proteome alterations in human endometriosis” by Dutta et al. .
Full Text Available Constant improvements in the field of surveying, computing and distribution of digital-content are reshaping the way Cultural Heritage can be digitised and virtually accessed, even remotely via web. A traditional 2D approach for data access, exploration, retrieval and exploration may generally suffice, however more complex analyses concerning spatial and temporal features require 3D tools, which, in some cases, have not yet been implemented or are not yet generally commercially available. Efficient organisation and integration strategies applicable to the wide array of heterogeneous data in the field of Cultural Heritage represent a hot research topic nowadays. This article presents a visualisation and query tool (QueryArch3D conceived to deal with multi-resolution 3D models. Geometric data are organised in successive levels of detail (LoD, provided with geometric and semantic hierarchies and enriched with attributes coming from external data sources. The visualisation and query front-end enables the 3D navigation of the models in a virtual environment, as well as the interaction with the objects by means of queries based on attributes or on geometries. The tool can be used as a standalone application, or served through the web. The characteristics of the research work, along with some implementation issues and the developed QueryArch3D tool will be discussed and presented.
Full Text Available Abstract Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows
Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.
There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…
Falquet, Laurent; Bordoli, Lorenza; Ioannidis, Vassilios; Pagni, Marco; Jongeneel, C Victor
EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a 'node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere else.
Bartocci, Ezio; Cacciagrano, Diletta; Di Berardini, Maria Rita; Merelli, Emanuela; Vito, Leonardo
The huge and dynamic amount of bioinformatic resources (e.g., data and tools) available nowadays in Internet represents a big challenge for biologists –for what concerns their management and visualization– and for bioinformaticians –for what concerns the possibility of rapidly creating and executing in-silico experiments involving resources and activities spread over the WWW hyperspace. Any framework aiming at integrating such resources as in a physical laboratory has imperatively to tackle –and possibly to handle in a transparent and uniform way– aspects concerning physical distribution, semantic heterogeneity, co-existence of different computational paradigms and, as a consequence, of different invocation interfaces (i.e., OGSA for Grid nodes, SOAP for Web Services, Java RMI for Java objects, etc.). The framework UBioLab has been just designed and developed as a prototype following the above objective. Several architectural features –as those ones of being fully Web-based and of combining domain ontologies, Semantic Web and workflow techniques– give evidence of an effort in such a direction. The integration of a semantic knowledge management system for distributed (bioinformatic) resources, a semantic-driven graphic environment for defining and monitoring ubiquitous workflows and an intelligent agent-based technology for their distributed execution allows UBioLab to be a semantic guide for bioinformaticians and biologists providing (i) a flexible environment for visualizing, organizing and inferring any (semantics and computational) "type" of domain knowledge (e.g., resources and activities, expressed in a declarative form), (ii) a powerful engine for defining and storing semantic-driven ubiquitous in-silico experiments on the domain hyperspace, as well as (iii) a transparent, automatic and distributed environment for correct experiment executions.
Schneider, M.V.; Watson, J.; Attwood, T.;
As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...
Full Text Available Abstract Background This paper proposes a novel framework for bioinformatics assisted biosurveillance and early warning to address the inefficiencies in traditional surveillance as well as the need for more timely and comprehensive infection monitoring and control. It leverages on breakthroughs in rapid, high-throughput molecular profiling of microorganisms and text mining. Results This framework combines the genetic and geographic data of a pathogen to reconstruct its history and to identify the migration routes through which the strains spread regionally and internationally. A pilot study of Salmonella typhimurium genotype clustering and temporospatial outbreak analysis demonstrated better discrimination power than traditional phage typing. Half of the outbreaks were detected in the first half of their duration. Conclusion The microbial profiling and biosurveillance focused text mining tools can enable integrated infectious disease outbreak detection and response environments based upon bioinformatics knowledge models and measured by outcomes including the accuracy and timeliness of outbreak detection.
Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.
Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.
Ghulam A. Parray
Full Text Available Saffron (Crocus sativus L. is a sterile triploid plant and belongs to the Iridaceae (Liliales, Monocots. Its genome is of relatively large size and is poorly characterized. Bioinformatics can play an enormous technical role in the sequence-level structural characterization of saffron genomic DNA. Bioinformatics tools can also help in appreciating the extent of diversity of various geographic or genetic groups of cultivated saffron to infer relationships between groups and accessions. The characterization of the transcriptome of saffron stigmas is the most vital for throwing light on the molecular basis of flavor, color biogenesis, genomic organization and biology of gynoecium of saffron. The information derived can be utilized for constructing biological pathways involved in the biosynthesis of principal components of saffron i.e., crocin, crocetin, safranal, picrocrocin and safchiA
Research in signaling networks contributes to a deeper understanding of organism living activities. With the development of experimental methods in the signal transduction field, more and more mechanisms of signaling pathways have been discovered. This paper introduces such popular bioin-formatics analysis methods for signaling networks as the common mechanism of signaling pathways and database resource on the Internet, summerizes the methods of analyzing the structural properties of networks, including structural Motif finding and automated pathways generation, and discusses the modeling and simulation of signaling networks in detail, as well as the research situation and tendency in this area. Now the investigation of signal transduction is developing from small-scale experiments to large-scale network analysis, and dynamic simulation of networks is closer to the real system. With the investigation going deeper than ever, the bioinformatics analysis of signal transduction would have immense space for development and application.
Yuen Macaire MS
Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First
Lakhno, V D
Mathematical biology and bioinformatics represent a new and rapidly progressing line of investigations which emerged in the course of work on the project "Human genome". The main applied problems of these sciences are grug design, patient-specific medicine and nanobioelectronics. It is shown that progress in the technology of mass sequencing of the human genome has set the stage for starting the national program on patient-specific medicine.
In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have been deciphered and are being exploited for fundamental research and applied to improve their breeding programs. The developments in sequencing technologies have also impacted the associated bioinformat...
Fang, Wai-Chi; Lue, Jaw-Chyng
A system comprising very-large-scale integrated (VLSI) circuits is being developed as a means of bioinformatics-oriented analysis and recognition of patterns of fluorescence generated in a microarray in an advanced, highly miniaturized, portable genetic-expression-assay instrument. Such an instrument implements an on-chip combination of polymerase chain reactions and electrochemical transduction for amplification and detection of deoxyribonucleic acid (DNA).
董永权; 李庆忠; 丁艳辉; 张永新
针对已有查询接口匹配方法匹配器权重设置困难、匹配决策缺乏有效处理的局限性,提出一种基于证据理论和任务分配的Deep Web查询接口匹配方法.该方法通过引人改进的D-S证据理论自动融合多个匹配器结果,避免手工设定匹配器权重,有效减少人工干预.通过对任务分配问题进行扩展,将查询接口的一对一匹配决策问题转化为扩展的任务分配问题,为源查询接口中的每一个属性选择合适的匹配,并在此基础上,采用树结构启发式规则进行一对多匹配决策.实验结果表明ETTA-IM方法具有较高的查准率和查全率.%To solve the limitations of existing query interface matching which have the difficulties of weight setting of the matcher and the absence of the efficient processing of matching decision, a deep web query interface matching approach based on evidence theory and task assignment is proposed called evidence theory and task assignment based query interface matching approach (ETTA-IM).Firstly, an improved D-S evidence theory is used to automatically combine multiple matchers.Thus, the weight of each matcher is not required to be set by hand and human involvement is reduced.Then, a method is used to select a proper attribute correspondence of each source attribute from target query interface, which converts one-to-one matching decision to the extended task assignment problem.Finally, based on one-to-one matching results, some heuristic rules of tree structure are used to perform one-to-many matching decision.Experimental results show that ETTA-IM approach has high precision and recall measure.
Lopes, Robson da Silva; Resende, Nathalia Maria; Honorio-França, Adenilda Cristina; França, Eduardo Luzía
Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through "omics" projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.
Robson da Silva Lopes
Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.
K Bretonnel Cohen
Full Text Available Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.
Orton, R J; Gu, Q; Hughes, J; Maabar, M; Modha, S; Vattipally, S B; Wilkie, G S; Davison, A J
The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing.
Cohen, K Bretonnel; Hunter, Lawrence E
Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.
Translational bioinformatics plays an indispensable role in transforming psychoneuroimmunology (PNI) into personalized medicine. It provides a powerful method to bridge the gaps between various knowledge domains in PNI and systems biology. Translational bioinformatics methods at various systems levels can facilitate pattern recognition, and expedite and validate the discovery of systemic biomarkers to allow their incorporation into clinical trials and outcome assessments. Analysis of the correlations between genotypes and phenotypes including the behavioral-based profiles will contribute to the transition from the disease-based medicine to human-centered medicine. Translational bioinformatics would also enable the establishment of predictive models for patient responses to diseases, vaccines, and drugs. In PNI research, the development of systems biology models such as those of the neurons would play a critical role. Methods based on data integration, data mining, and knowledge representation are essential elements in building health information systems such as electronic health records and computerized decision support systems. Data integration of genes, pathophysiology, and behaviors are needed for a broad range of PNI studies. Knowledge discovery approaches such as network-based systems biology methods are valuable in studying the cross-talks among pathways in various brain regions involved in disorders such as Alzheimer's disease.
Friedrich, Andreas; Kenar, Erhan; Kohlbacher, Oliver; Nahnsen, Sven
Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.
肖斌; 蒋宇全; 董士海
System architecture and design features of a web browser based multimodal prototype system——NetShop is introduced. It is designed for netshopping applications. We use the context-based interactive query, principal modality driven multimodal integration policy, remedy input and multimodal output to provide a natural interactive environment for this kind of applications. Furthermore, we develop an open speech programming interface using the plugin and liveconnect technology. It not only helps to enhance the flexibility of the whole system, but also provides an easy way for the third party to develop speech enabled web based applications.%介绍了一个基于Web浏览器的多通道网上购物界面NetShop原型系统的系统结构及设计特点.这一系统是在对通用Web浏览器的多通道扩充的基础上，以网上购物为背景设计的多通道交互系统.系统通过采取基于上下文的查询、基于主通道的整合策略、语音反馈及补偿性输入等手段，为网上购物提供了一个自然的交互环境.在系统结构上采用了软插件技术，使得设计更为灵活，并为第三方的开发提供了一个开放性的接口.
Mei, Yongguo; Carbo, Adria; Hoops, Stefan; Hontecillas, Raquel; Bassaganya-Riera, Josep
Modeling and simulations approaches have been widely used in computational biology, mathematics, bioinformatics and engineering to represent complex existing knowledge and to effectively generate novel hypotheses. While deterministic modeling strategies are widely used in computational biology, stochastic modeling techniques are not as popular due to a lack of user-friendly tools. This paper presents ENISI SDE, a novel web-based modeling tool with stochastic differential equations. ENISI SDE provides user-friendly web user interfaces to facilitate adoption by immunologists and computational biologists. This work provides three major contributions: (1) discussion of SDE as a generic approach for stochastic modeling in computational biology; (2) development of ENISI SDE, a web-based user-friendly SDE modeling tool that highly resembles regular ODE-based modeling; (3) applying ENISI SDE modeling tool through a use case for studying stochastic sources of cell heterogeneity in the context of CD4+ T cell differentiation. The CD4+ T cell differential ODE model has been published  and can be downloaded from biomodels.net. The case study reproduces a biological phenomenon that is not captured by the previously published ODE model and shows the effectiveness of SDE as a stochastic modeling approach in biology in general and immunology in particular and the power of ENISI SDE.
Weniger, Thomas; Krawczyk, Justina; Supply, Philip; Niemann, Stefan; Harmsen, Dag
Harmonized typing of bacteria and easy identification of locally or internationally circulating clones are essential for epidemiological surveillance and disease control. For Mycobacterium tuberculosis complex (MTBC) species, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible and discriminatory typing method. However, no specialized bioinformatics web tools are available for analysing MLVA data in combination with other, complementary typing data. Therefore, we have developed the web application MIRU-VNTRplus (http://www.miru-vntrplus.org). This freely accessible service allows users to analyse genotyping data of their strains alone or in comparison with a reference database of strains representing the major MTBC lineages. Analysis and comparisons of genotypes can be based on MLVA-, spoligotype-, large sequence polymorphism and single nucleotide polymorphism data, or on a weighted combination of these markers. Tools for data exploration include search for similar strains, creation of phylogenetic and minimum spanning trees and mapping of geographic information. To facilitate scientific communication, an expanding genotype nomenclature (MLVA MtbC15-9 type) that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions.
With a number of cheap commercial dry EEG kits available today, it is possible to look at user attention driven scenarios for interaction with the web browser. Using EEG to determine the user's attention level is preferable to using methods such as gaze tracking or time spent on the webpage. In this paper we use the attention level in three different ways. First, as a control mechanism, to control user interface elements such as menus or buttons. Second, to make the web browser responsive to ...
Candey, Robert M.; Harris, Bernard T.; Chimiak, Reine A.
The Space Physics Data Facility (SPDF) Web services provides a distributed programming interface to a portion of the SPDF software. (A general description of Web services is available at http://www.w3.org/ and in many current software-engineering texts and articles focused on distributed programming.) The SPDF Web services distributed programming interface enables additional collaboration and integration of the SPDF software system with other software systems, in furtherance of the SPDF mission to lead collaborative efforts in the collection and utilization of space physics data and mathematical models. This programming interface conforms to all applicable Web services specifications of the World Wide Web Consortium. The interface is specified by a Web Services Description Language (WSDL) file. The SPDF Web services software consists of the following components: 1) A server program for implementation of the Web services; and 2) A software developer s kit that consists of a WSDL file, a less formal description of the interface, a Java class library (which further eases development of Java-based client software), and Java source code for an example client program that illustrates the use of the interface.
Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer;
The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially...... within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them...
Robbins Kay A
Full Text Available Abstract Background Many bioinformatics algorithms and data sets are deployed using web services so that the results can be explored via the Internet and easily integrated into other tools and services. These services often include data from other sites that is accessed either dynamically or through file downloads. Developers of these services face several problems because of the dynamic nature of the information from the upstream services. Many publicly available repositories of bioinformatics data frequently update their information. When such an update occurs, the developers of the downstream service may also need to update. For file downloads, this process is typically performed manually followed by web service restart. Requests for information obtained by dynamic access of upstream sources is sometimes subject to rate restrictions. Findings SideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating. Conclusions We have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.
Query interface schema matching is a key step in Deep Web data integration. Dual Correlated Mining (DCM) is able to make full use of association mining method to solve the problems of complex interface schema matching. There are some problems about DCM, such as inefficiency and inaccuracy in matching. Therefore, a new method based on matching degree and semantic similarity was presented in this paper to solve the problems. Firstly, the method used correlation matrix to save the association relationship among attributes; and then, matching degree was applied to calculate the degree of correlation between attributes; at last, semantic similarity was used to ensure the accuracy of final results. The experimental results on BAMM data sets of University of Illinois show that the proposed method has higher precision and efficiency than DCM and improved DCM, and indicate that the method can deal with the query interface schema matching problems very well.%查询接口模式匹配是Deep Web信息集成中的关键部分,双重相关性挖掘方法(DCM)能有效利用关联挖掘方法解决复杂接口模式匹配问题.针对DCM方法在匹配效率、匹配准确性方面的不足,提出了一种基于匹配度和语义相似度的新模式匹配方法.该方法首先使用矩阵存储属性间的关联关系,然后采用匹配度计算属性间的相关度,最后利用语义相似度计算候选匹配的相似性.通过在美国伊利诺斯大学的BAMM数据集上进行实验,所提方法与DCM及其改进方法比较有更高的匹配效率和准确性,表明该方法能更好地处理接口之间模式匹配问题.
Asem KASEM; Tetsuo IDA
We present a computing environment for ori-gami on the web. The environment consists of the compu-tational origami engine Eos for origami construction, visualization, and geometrical reasoning, WEвEOS for pro-viding web interface to the functionalities of Eos, and web service system SCORUM for symbolic computing web ser-vices. WEBEOS is developed using Web2.0 technologies, and provides a graphical interactive web interface for ori-gami construction and proving. In SCORUM, we are prepar-ing web services for a wide range of symbolic computing systems, and are using these services in our origami envir-onment. We explain the functionalities of this environment, and discuss its architectural and technological features.
The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.
Lue, Jaw-Chyng L.; Fang, Wai-Chi
A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.
Handl, Julia; Kell, Douglas B; Knowles, Joshua
This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.
Alkema, Wynand; Boekhorst, Jos; Wels, Michiel; van Hijum, Sacha A F T
In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.
Jessica D. Tenenbaum
Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex-tualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field.
The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.
Full Text Available Abstract Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds
Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari
Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…
Pravin Dudhagara; Sunil Bhavsar; Chintan Bhagat; Anjana Ghelani; Shreyas Bhatt; Rajesh Patel
The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.
Full Text Available The development of next-generation sequencing (NGS platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.
Dudhagara, Pravin; Bhavsar, Sunil; Bhagat, Chintan; Ghelani, Anjana; Bhatt, Shreyas; Patel, Rajesh
The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.
The University of Arizona Artificial Intelligence Lab (AI Lab) Dark Web project is a long-term scientific research program that aims to study and understand the international terrorism (Jihadist) phenomena via a computational, data-centric approach. We aim to collect "ALL" web content generated by international terrorist groups, including web sites, forums, chat rooms, blogs, social networking sites, videos, virtual world, etc. We have developed various multilingual data mining, text mining, and web mining techniques to perform link analysis, content analysis, web metrics (technical
Bohonak Andrew J; Jensen Jeffrey L; Kelley Scott T
Abstract Background The population genetic pattern known as "isolation by distance" results from spatially limited gene flow and is a commonly observed phenomenon in natural populations. However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly. Results We have created Isolation by Distance Web Service (IBDWS) a user-friendly web interface for determining patterns of isolation by distance. Using this site, ...
Charoentong, Pornpimol; Angelova, Mihaela; Efremova, Mirjana; Gallasch, Ralf; Hackl, Hubert; Galon, Jerome; Trajanoski, Zlatko
Recent mechanistic insights obtained from preclinical studies and the approval of the first immunotherapies has motivated increasing number of academic investigators and pharmaceutical/biotech companies to further elucidate the role of immunity in tumor pathogenesis and to reconsider the role of immunotherapy. Additionally, technological advances (e.g., next-generation sequencing) are providing unprecedented opportunities to draw a comprehensive picture of the tumor genomics landscape and ultimately enable individualized treatment. However, the increasing complexity of the generated data and the plethora of bioinformatics methods and tools pose considerable challenges to both tumor immunologists and clinical oncologists. In this review, we describe current concepts and future challenges for the management and analysis of data for cancer immunology and immunotherapy. We first highlight publicly available databases with specific focus on cancer immunology including databases for somatic mutations and epitope databases. We then give an overview of the bioinformatics methods for the analysis of next-generation sequencing data (whole-genome and exome sequencing), epitope prediction tools as well as methods for integrative data analysis and network modeling. Mathematical models are powerful tools that can predict and explain important patterns in the genetic and clinical progression of cancer. Therefore, a survey of mathematical models for tumor evolution and tumor-immune cell interaction is included. Finally, we discuss future challenges for individualized immunotherapy and suggest how a combined computational/experimental approaches can lead to new insights into the molecular mechanisms of cancer, improved diagnosis, and prognosis of the disease and pinpoint novel therapeutic targets.
A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....
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.
Abla, G., E-mail: firstname.lastname@example.org [General Atomics, P.O. Box 85608, San Diego, CA (United States); Kim, E.N.; Schissel, D.P.; Flanagan, S.M. [General Atomics, P.O. Box 85608, San Diego, CA (United States)
Web browsers have become a major application interface for participating in scientific experiments such as those in magnetic fusion. The recent advances in web technologies motivated the deployment of interactive web applications with rich features. In the scientific world, web applications have been deployed in portal environments. When used in a scientific research environment, such as fusion experiments, web portals can present diverse sources of information in a unified interface. However, the design and development of a scientific web portal has its own challenges. One such challenge is that a web portal needs to be fast and interactive despite the high volume of information and number of tools it presents. Another challenge is that the visual output of the web portal must not be overwhelming to the end users, despite the high volume of data generated by fusion experiments. Therefore, the applications and information should be customizable depending on the needs of end users. In order to meet these challenges, the design and implementation of a web portal needs to support high interactivity and user customization. A web portal has been designed to support the experimental activities of DIII-D researchers worldwide by providing multiple services, such as real-time experiment status monitoring, diagnostic data access and interactive data visualization. The web portal also supports interactive collaborations by providing a collaborative logbook, shared visualization and online instant messaging services. The portal's design utilizes the multi-tier software architecture and has been implemented utilizing web 2.0 technologies, such as AJAX, Django, and Memcached, to develop a highly interactive and customizable user interface. It offers a customizable interface with personalized page layouts and list of services, which allows users to create a unique, personalized working environment to fit their own needs and interests. This paper describes the software
de Matos, Paula; Cham, Jennifer A; Cao, Hong; Alcántara, Rafael; Rowland, Francis; Lopez, Rodrigo; Steinbeck, Christoph
User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, 'canvas sort' card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.
Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.
Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…
Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.
At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…
Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…
@@ The Studio of Computational Biology & Bioinformatics (SCBB), IHBT, CSIR,Palampur, India organized one of the very first national workshop funded by DBT,Govt.of India, on the Bioinformatics issues associated with next generation sequencing approaches.The course structure was designed by SCBB, IHBT.The workshop took place in the IHBT premise on 17 and 18 June 2010.
Nomi L Harris
Full Text Available The Bioinformatics Open Source Conference (BOSC is organized by the Open Bioinformatics Foundation (OBF, a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG before the annual Intelligent Systems in Molecular Biology (ISMB conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.
Wong, Stephen T. C.; Patwardhan, Anil
The evolution of biology into a large-scale quantitative molecular science has been paralleled by concomitant advances in computer storage systems, processing power, and data-analysis algorithms. The application of computer technologies to molecular biology data has given rise to a new system-based approach to biological research. Bioinformatics addresses problems related to the storage, retrieval and analysis of information about biological structure, sequence and function. Its goals include the development of integrated storage systems and analysis tools to interpret molecular biology data in a biologically meaningful manner in normal and disease processes and in efforts for drug discovery. This paper reviews recent developments in data management, storage, and retrieval that are central to the effective use of structural and functional genomics in fulfilling these goals.
Handel, Adam E.
Estrogen is a steroid hormone that plays critical roles in a myriad of intracellular pathways. The expression of many genes is regulated through the steroid hormone receptors ESR1 and ESR2. These bind to DNA and modulate the expression of target genes. Identification of estrogen target genes is greatly facilitated by the use of transcriptomic methods, such as RNA-seq and expression microarrays, and chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq). Combining transcriptomic and ChIP-seq data enables a distinction to be drawn between direct and indirect estrogen target genes. This chapter will discuss some methods of identifying estrogen target genes that do not require any expertise in programming languages or complex bioinformatics. PMID:26585125
ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...
In the last ten years, high-performance and massively parallel computing technology comes into a high speed developing phase and is used in all fields. The cluster computer systems are also being widely used for their low cost and high performance. In bioinformatics research, solving a problem with computer usually takes hours even days. To speed up research, high-performance cluster computers are considered to be a good platform. Moving into the new MPP (massively parallel processing) system, the original algorithm should be parallelized in a proper way. In this paper, a new parallelizing method of useful sequence alignment algorithm (Smith-Waterman) is designed based on its optimizing algorithm already exists. The result is gratifying.
van Driel Marc A
Full Text Available Abstract With the explosion in genomic and functional genomics information, methods for disease gene identification are rapidly evolving. Databases are now essential to the process of selecting candidate disease genes. Combining positional information with disease characteristics and functional information is the usual strategy by which candidate disease genes are selected. Enrichment for candidate disease genes, however, depends on the skills of the operating researcher. Over the past few years, a number of bioinformatics methods that enrich for the most likely candidate disease genes have been developed. Such in silico prioritisation methods may further improve by completion of datasets, by development of standardised ontologies across databases and species and, ultimately, by the integration of different strategies.
Huurdeman, H.C.; Ben David, A.; Samar, T.
Web archives provide access to snapshots of the Web of the past, and could be valuable for research purposes. However, access to these archives is often limited, both in terms of data availability, and interfaces to this data. This paper explores new methods to overcome these limitations. It present
Herman, I.; Gylling, M.
Although using advanced Web technologies at their core, e-books represent a parallel universe to everyday Web documents. Their production workflows, user interfaces, their security, access, or privacy models, etc, are all distinct. There is a lack of a vision on how to unify Digital Publishing and t
Cohen, A.R.; Vitányi, P.M.B.
Normalized web distance (NWD) is a similarity or normalized semantic distance based on the World Wide Web or any other large electronic database, for instance Wikipedia, and a search engine that returns reliable aggregate page counts. For sets of search terms the NWD gives a similarity on a scale fr
Drijfhout, Wanno; Oliver, Jundt; Wevers, Lesley; Hiemstra, Djoerd
We use Common Crawl's 25TB data set of web pages to construct a database of associated concepts using Hadoop. The database can be queried through a web application with two query interfaces. A textual interface allows searching for similarities and differences between multiple concepts using a query
Ponyik, Joseph G.; York, David W.
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.
Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla
RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/.
Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.
Dragut, Eduard Constantin
An increasing number of Web sites expose their content via query interfaces, many of them offering the same type of products/services (e.g., flight tickets, car rental/purchasing). They constitute the so-called "Deep Web". Accessing the content on the Deep Web has been a long-standing challenge for the database community. For a user interested in…
Paraskevopoulou, Maria D; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A G
MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.
Full Text Available On World Wide Web various kind of content are generated in huge amount, so to give relevant result to user web recommendation become important part of web application. On web different kind of web recommendation are made available to user every day that includes Image, Video, Audio, query suggestion and web page. In this paper we are aiming at providing framework for web page recommendation. 1 First we describe the basics of web mining, types of web mining. 2 Details of each web mining technique.3We propose the architecture for the personalized web page recommendation.
Semantic Web Services for Web Databases introduces an end-to-end framework for querying Web databases using novel Web service querying techniques. This includes a detailed framework for the query infrastructure for Web databases and services. Case studies are covered in the last section of this book. Semantic Web Services For Web Databases is designed for practitioners and researchers focused on service-oriented computing and Web databases.
Obrenovic, Z.; Ossenbruggen, J.R. van
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,
Full Text Available The information on the web is growing dramatically. The users has to spend lots of time on the web finding the information they are interested in. Today, he traditional search engines do not give users enough personalized help but provide the user with lots of irrelevant information. In this paper, we present a personalize Web searchsystem, which can helps users to get the relevant web pages based on their selection from the domain list. Thus, users can obtain a set of interested domains and the web pages from the system. The system is based on features extracted from hyperlinks, such as anchor terms or URL tokens. Our methodology uses an innovative weighted URL Rank algorithm based on user interested domains and user query.
Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.
Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and backgrounds of a diverse set of students, predominantly computer science and biology undergraduate and graduate students. Although the researchers desired to investigate student views of the course, they were interested in the potentially different perspectives. Q methodology, a measure of subjectivity, allowed the researchers to determine the various student perspectives in the bioinformatics course.
Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke
Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics.
Auerbach, Raymond K
The sciences have seen a large increase in demand for students in bioinformatics and multidisciplinary fields in general. Many new educational programs have been created to satisfy this demand, but navigating these programs requires a non-traditional outlook and emphasizes working in teams of individuals with distinct yet complementary skill sets. Written from the perspective of a current bioinformatics student, this article seeks to offer advice to prospective and current students in bioinformatics regarding what to expect in their educational program, how multidisciplinary fields differ from more traditional paths, and decisions that they will face on the road to becoming successful, productive bioinformaticists.
由于GIS中不但涉及属性数据，而且还涉及地理空间数据，因此数据量相对庞大，所以在设计和实现WebGIS时。必须考虑其性能问题．为了更高效地实现基于WebService的WebGIS的相关功能，有必要对其性能进行优化，这可通过增大Web Service颗粒度，不使用XML作为WebGIS系统内部的接口，压缩SOAP，通过异步访问服务器端Web Service中的Web方法，优化数据库，使用客户端和服务器端缓存等一系列优化措施来加快数据的访问速度，减轻网络传输负载，提高基于Web Service的WebGIS性能．%It not only includes attribute data in the CIS, but also includes the geo-spatial data, arelatively large amount of data, so we must consider the performance issues in the design and implementation of WebGIS. In order to more efficiently＂ implement the relative functions of a WebGIS based on Web Service, it is necessary to optimize the performance, which can increase the particle size of Web Service, do not use XML as the WebGIS interface within the system; compressed SOAP, an asynchronous Access Web method in Web Service of server-side, optimizing the database, using the client and server side caching and a series of optimization measures to speed up data access speed and reduce network traffic loads and improve the performance of WebGIS based on Web Service.
Delin, Kevin A. (Inventor); Jackson, Shannon P. (Inventor)
A Sensor Web formed of a number of different sensor pods. Each of the sensor pods include a clock which is synchronized with a master clock so that all of the sensor pods in the Web have a synchronized clock. The synchronization is carried out by first using a coarse synchronization which takes less power, and subsequently carrying out a fine synchronization to make a fine sync of all the pods on the Web. After the synchronization, the pods ping their neighbors to determine which pods are listening and responded, and then only listen during time slots corresponding to those pods which respond.
GAO; George; Fu
Highly pathogenic influenza A virus H5N1 has spread out worldwide and raised the public concerns. This increased the output of influenza virus sequence data as well as the research publication and other reports. In order to fight against H5N1 avian flu in a comprehensive way, we designed and started to set up the Website for Avian Flu Information (http://www.avian-flu.info) from 2004. Other than the influenza virus database available, the website is aiming to integrate diversified information for both researchers and the public. From 2004 to 2009, we collected information from all aspects, i.e. reports of outbreaks, scientific publications and editorials, policies for prevention, medicines and vaccines, clinic and diagnosis. Except for publications, all information is in Chinese. Till April 15, 2009, the cumulative news entries had been over 2000 and research papers were approaching 5000. By using the curated data from Influenza Virus Resource, we have set up an influenza virus sequence database and a bioinformatic platform, providing the basic functions for the sequence analysis of influenza virus. We will focus on the collection of experimental data and results as well as the integration of the data from the geological information system and avian influenza epidemiology.
LIU Di; LIU Quan-He; WU Lin-Huan; LIU Bin; WU Jun; LAO Yi-Mei; LI Xiao-Jing; GAO George Fu; MA Jun-Cai
Highly pathogenic influenza A virus H5N1 has spread out worldwide and raised the public concerns. This increased the output of influenza virus sequence data as well as the research publication and other reports. In order to fight against H5N1 avian flu in a comprehensive way, we designed and started to set up the Website for Avian Flu Information (http://www.avian-flu.info) from 2004. Other than the influenza virus database available, the website is aiming to integrate diversified information for both researchers and the public. From 2004 to 2009, we collected information from all aspects, i.e. reports of outbreaks, scientific publications and editorials, policies for prevention, medicines and vaccines, clinic and diagnosis. Except for publications, all information is in Chinese. Till April 15, 2009, the cumulative news entries had been over 2000 and research papers were approaching 5000. By using the curated data from Influenza Virus Resource, we have set up an influenza virus sequence database and a bioin-formatic platform, providing the basic functions for the sequence analysis of influenza virus. We will focus on the collection of experimental data and results as well as the integration of the data from the geological information system and avian influenza epidemiology.
Tabbers, H.; Kester, L.; Hummel, H.; Nadolski, R.; Jochems, W.; Merriënboer, J.; Koper, R.
An important question in web-based education is how to deal with the design of the interface. What will the actual screen look like? Two main issues that are especially relevant for educational purposes are discussed, both from a Human-Computer Interaction and an Educational Psychology perspective.
Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael JE
Summary Phyre2 is a suite of tools available on the web to predict and analyse protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a protocol. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyse the effect of amino-acid variants (e.g. nsSNPs) for a user’s protein sequence. Users are guided through results by a simple interface at a level of detail determined by them. This protocol will guide a user from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30mins and 2 hours after submission. PMID:25950237
Romano, D.; Pinzger, M.
Preprint of paper published in: ICWS 2012 - IEEE 19th International Conference on Web Services, 24-29 June 2012; doi:10.1109/ICWS.2012.29 In the service-oriented paradigm web service interfaces are considered contracts between web service subscribers and providers. However, these interfaces are co
Vandervalk, Ben P; McCarthy, E Luke; Wilkinson, Mark D
Facile and meaningful integration of data from disparate resources is the 'holy grail' of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized 'semantic warehouses' that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the 'Deep Web'-that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine 'The State of the Union' for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.
Mathe, Z.; Casajus Ramo, A.; Lazovsky, N.; Stagni, F.
For many years the DIRAC interware (Distributed Infrastructure with Remote Agent Control) has had a web interface, allowing the users to monitor DIRAC activities and also interact with the system. Since then many new web technologies have emerged, therefore a redesign and a new implementation of the DIRAC Web portal were necessary, taking into account the lessons learnt using the old portal. These new technologies allowed to build a more compact, robust and responsive web interface that enables users to have better control over the whole system while keeping a simple interface. The web framework provides a large set of “applications”, each of which can be used for interacting with various parts of the system. Communities can also create their own set of personalised web applications, and can easily extend already existing ones with a minimal effort. Each user can configure and personalise the view for each application and save it using the DIRAC User Profile service as RESTful state provider, instead of using cookies. The owner of a view can share it with other users or within a user community. Compatibility between different browsers is assured, as well as with mobile versions. In this paper, we present the new DIRAC Web framework as well as the LHCb extension of the DIRAC Web portal.
Graham, Matthew; Rixon, Guy; Grid andWeb Services Working Group; Graham, Matthew; Rixon, Guy
This document describes the minimum interface that a (SOAP- or REST-based) web service requires to participate in the IVOA. Note that this is not required of standard VO services developed prior to this specification, although uptake is strongly encouraged on any subsequent revision. All new standard VO services, however, must feature a VOSI-compliant interface.
Reviews the development of scalable pattern recognition algorithms for computational biology and bioinformatics Includes numerous examples and experimental results to support the theoretical concepts described Concludes each chapter with directions for future research and a comprehensive bibliography
Gentleman, R.C.; Carey, V.J.; Bates, D.M.;
into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....
目的:研究生物信息学起源、发展趋势,与其他学科相互交叉渗透关系的发展及强度.方法:利用美国《科学引文索引》(SCI)数据库web of science,运用文献计量学方法对8种权威生物信息学期刊2001年至2010年于2011年1月15日之前上传至web of science的全部文献进行统计及分析.通过研究生物信息学相关论文的主题分类,被引情况及施引文献的分类,寻找其跨学科的趋势及相关研究领域的进展情况、主要内容.结果:生物信息学的相关文献数在2001-2010间逐年增加,在2009-2010年达到高峰.跨学科领域广泛,并以生物化学、分子生物学、计算生物学、微生物学、数学、统计学等学科为主要交叉学科.各交叉学科与生物信息学之间跨学科研究的文献数也呈逐年递增趋势.结论:生物信息学的跨学科范围广泛,发展迅速.%Objective:To study the origin, developing trends of bioinformatics, relationship with other disciplines, the intensity and development of interdisciplinary situation. Methods: In this paper, the United States "Science Citation Index" (SCI) database, web of science, and the method of bibliometrics are used to do a research about all literature from 8 authoritative bioinformatics journals from the year 2001 to 2010 with metrology statistics. Through researches about the classification related to the theme of the papers of the literature, and the classification of cited literature's discipline, the trends and the research areas of bioinformatics1 inter-disciplinary development can be known. Results: Bioinformatics literature in the decade from 2001 to 2010 is increased year by year and reached a peak in 2009 and 2010 year. The interdisciplinary fields of bioinformatics become wider. Among all the interdisciplinary fields, biochemistry, molecular biology, computational biology, microbiology, mathematics, statistics and other disciplines are the main cross-disciplinary disciplines
Keane, Thomas M; Page, Andrew J.; McInerney, James O; Naughton, Thomas J.
In the past number of years the demand for high performance computing has greatly increased in the area of bioinformatics. The huge increase in size of many genomic databases has meant that many common tasks in bioinformatics are not possible to complete in a reasonable amount of time on a single processor. Recently distributed computing has emerged as an inexpensive alternative to dedicated parallel computing. We have developed a general-purpose distributed computing platform ...
Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work
Fernández Villamor, José Ignacio; Blasco Garcia, Jacobo; Iglesias Fernandez, Carlos Angel; Garijo Ayestaran, Mercedes
In spite of the increasing presence of Semantic Web Facilities, only a limited amount of the available resources in the Internet provide a semantic access. Recent initiatives such as the emerging Linked Data Web are providing semantic access to available data by porting existing resources to the semantic web using different technologies, such as database-semantic mapping and scraping. Nevertheless, existing scraping solutions are based on ad-hoc solutions complemented with graphical interface...
Hoon, Shawn; Ratnapu, Kiran Kumar; Chia, Jer-Ming; Kumarasamy, Balamurugan; Juguang, Xiao; Clamp, Michele; Stabenau, Arne; Potter, Simon; Clarke, Laura; Stupka, Elia
We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data residing in a federation of databases that, in turn, come in different formats and modes of accessibility. Secondly, the tsunami of data to be handled will require robust systems that enable bioinformatics analysis to be carried out in a parallel fashion. Thirdly, the ever-evolving state of bioinformatics presents new algorithms and paradigms in conducting analysis. This means that any bioinformatics framework must be flexible and generic enough to accommodate such changes. In addition, we identify the need for introducing an explicit protocol-based approach to bioinformatics analysis that will lend rigorousness to the analysis. This makes it easier for experimentation and replication of results by external parties. Biopipe is designed in an effort to meet these goals. It aims to allow researchers to focus on protocol design. At the same time, it is designed to work over a compute farm and thus provides high-throughput performance. A common exchange format that encapsulates the entire protocol in terms of the analysis modules, parameters, and data versions has been developed to provide a powerful way in which to distribute and reproduce results. This will enable researchers to discuss and interpret the data better as the once implicit assumptions are now explicitly defined within the Biopipe framework.
Telles Guilherme P.
Full Text Available The Sugarcane EST project (SUCEST produced 291,904 expressed sequence tags (ESTs in a consortium that involved 74 sequencing and data mining laboratories. We created a web site for this project that served as a ?meeting point? for receiving, processing, analyzing, and providing services to help explore the sequence data. In this paper we describe the information pathway that we implemented to support this project and a brief explanation of the clustering procedure, which resulted in 43,141 clusters.
and dhurrin, which have not previously been characterized in blueberries. There are more than 44,500 spider species with distinct habitats and unique characteristics. Spiders are masters of producing silk webs to catch prey and using venom to neutralize. The exploration of the genetics behind these properties...... has just started. We have assembled and annotated the first two spider genomes to facilitate our understanding of spiders at the molecular level. The need for analyzing the large and increasing amount of sequencing data has increased the demand for efficient, user friendly, and broadly applicable...
Full Text Available Abstract Background It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opportunity for pathogen detection and discovery in human tissues but requires development of new genome-wide bioinformatics tools. Results Here we present CaPSID (Computational Pathogen Sequence IDentification, a comprehensive bioinformatics platform for identifying, querying and visualizing both exogenous and endogenous pathogen nucleotide sequences in tumor genomes and transcriptomes. CaPSID includes a scalable, high performance database for data storage and a web application that integrates the genome browser JBrowse. CaPSID also provides useful metrics for sequence analysis of pre-aligned BAM files, such as gene and genome coverage, and is optimized to run efficiently on multiprocessor computers with low memory usage. Conclusions To demonstrate the usefulness and efficiency of CaPSID, we carried out a comprehensive analysis of both a simulated dataset and transcriptome samples from ovarian cancer. CaPSID correctly identified all of the human and pathogen sequences in the simulated dataset, while in the ovarian dataset CaPSID’s predictions were successfully validated in vitro.
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.
Full Text Available Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO in the Web Ontology Language (OWL format.
Gillies, Kim; Roberts, Scott; Brighton, Allan; Rogers, John
The TMT Software System consists of software components that interact with one another through a software infrastructure called TMT Common Software (CSW). CSW consists of software services and library code that is used by developers to create the subsystems and components that participate in the software system. CSW also defines the types of components that can be constructed and their roles. The use of common component types and shared middleware services allows standardized software interfaces for the components. A software system called the TMT Interface Database System was constructed to support the documentation of the interfaces for components based on CSW. The programmer describes a subsystem and each of its components using JSON-style text files. A command interface file describes each command a component can receive and any commands a component sends. The event interface files describe status, alarms, and events a component publishes and status and events subscribed to by a component. A web application was created to provide a user interface for the required features. Files are ingested into the software system's database. The user interface allows browsing subsystem interfaces, publishing versions of subsystem interfaces, and constructing and publishing interface control documents that consist of the intersection of two subsystem interfaces. All published subsystem interfaces and interface control documents are versioned for configuration control and follow the standard TMT change control processes. Subsystem interfaces and interface control documents can be visualized in the browser or exported as PDF files.
The perfect place to learn how to design Web sites for mobile devices!. With the popularity of Internet access via cell phones and other mobile devices, Web designers now have to consider as many as eight operating systems, several browsers, and a slew of new devices as they plan a new site, a new interface, or a new sub-site. This easy-to-follow friendly book guides you through this brave new world with a clear look at the fundamentals and offers practical techniques and tricks you may not have considered.: Explores all issues to consider in planning a mobile site; Covers the tools needed for
Full Text Available Interface dermatitis includes diseases in which the primary pathology involves the dermo-epidermal junction. The salient histological findings include basal cell vacuolization, apoptotic keratinocytes (colloid or Civatte bodies, and obscuring of the dermo-epidermal junction by inflammatory cells. Secondary changes of the epidermis and papillary dermis along with type, distribution and density of inflammatory cells are used for the differential diagnoses of the various diseases that exhibit interface changes. Lupus erythematosus, dermatomyositis, lichen planus, graft versus host disease, erythema multiforme, fixed drug eruptions, lichen striatus, and pityriasis lichenoides are considered major interface diseases. Several other diseases (inflammatory, infective, and neoplastic may show interface changes.
Machluf, Yossy; Yarden, Anat
Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.
Obrenovic, Z.; Ossenbruggen, J.R. van
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,
Full Text Available Abstract Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.
Full Text Available Abstract Background As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. Results COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. Conclusions The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.
Marylene S. Eder
Full Text Available Abstract Interactive campus map is a web based application that can be accessed through a web browser. With the Google Map Application Programming Interface availability of the overlay function has been taken advantage to create custom map functionalities. Collection of building points were gathered for routing and to create polygons which serves as a representation of each building. The previous campus map provides a static visual representation of the campus. It uses legends building name and its corresponding building number in providing information. Due to its limited capabilities it became a realization to the researchers to create an interactive campus map.Storing data about the building room and staff information and university events and campus guide are among the primary features that this study has to offer. Interactive Web-based Campus Information System is intended in providing a Campus Information System.It is open to constant updates user-friendly for both trained and untrained users and capable of responding to all needs of users and carrying out analyses. Based on the data gathered through questionnaires researchers analyzed the results of the test survey and proved that the system is user friendly deliver information to users and the important features that the students expect.
Ravn, Anders P.; Staunstrup, Jørgen
This paper proposes a model for specifying interfaces between concurrently executing modules of a computing system. The model does not prescribe a particular type of communication protocol and is aimed at describing interfaces between both software and hardware modules or a combination of the two...
Hansen, Klaus Marius
Fluid interaction, interaction by the user with the system that causes few breakdowns, is essential to many user interfaces. We present two concrete software systems that try to support fluid interaction for different work practices. Furthermore, we present specificity, generality, and minimality...... as design goals for fluid interfaces....
Holbøll, Joachim T.; Henriksen, Mogens; Nilson, Jesper K.;
The wide use of solid insulating materials combinations in combinations has introduced problems in the interfaces between components. The most common insulating materials are cross-linked polyethylene (XLPE), silicone rubber (SIR) and ethylene-propylene rubbers (EPR). Assemblies of these materials...... have caused major failures. In the Netherlands, a major black out was caused by interface problems in 150kV cable terminations, causing a cascade of breakdowns. There is a need to investigate the reasons for this and other similar breakdowns.The major problem is expected to lie in the interface between...... two different materials. Environmental influence, surface treatment, defects in materials and interface, design, pressure and rubbing are believed to have an effect on interface degradation. These factors are believed to increase the possibility of partial discharges (PD). PD will, with time, destroy...
Full Text Available Abstract Background Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III of 3.96 million single nucleotide polymorphisms (SNPs in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL analysis. Results SNPexp is implemented as a server-side script, and publicly available on this website: http://tinyurl.com/snpexp. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results. Conclusions SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets.
García Populin, Iván
Trabajo final de carrera desarrollado en .NET. Presenta un gestor de contenidos web para generar una web publicitaria. Treball final de carrera desenvolupat en .NET. Presenta un gestor de continguts web per generar una web publicitària.
Sweeney, Edwina; Curran, Kevin; Xie, Ermai
A Web crawler or spider crawls through the Web looking for pages to index, and when it locates a new page it passes the page on to an indexer. The indexer identifies links, keywords, and other content and stores these within its database. This database is searched by entering keywords through an interface and suitable Web pages are returned in a results page in the form of hyperlinks accompanied by short descriptions. The Web, however, is increasingly moving away from being a collection of documents to a multidimensional repository for sounds, images, audio, and other formats. This is leading to a situation where certain parts of the Web are invisible or hidden. The term known as the "Deep Web" has emerged to refer to the mass of information that can be accessed via the Web but cannot be indexed by conventional search engines. The concept of the Deep Web makes searches quite complex for search engines. Google states that the claim that conventional search engines cannot find such documents as PDFs, Word, PowerPoint, Excel, or any non-HTML page is not fully accurate and steps have been taken to address this problem by implementing procedures to search items such as academic publications, news, blogs, videos, books, and real-time information. However, Google still only provides access to a fraction of the Deep Web. This chapter explores the Deep Web and the current tools available in accessing it.
Coassin, Stefan; Brandstätter, Anita; Kronenberg, Florian
Genome-wide association studies (GWASs) led to impressive advances in the elucidation of genetic factors underlying complex phenotypes and diseases. However, the ability of GWAS to identify new susceptibility loci in a hypothesis-free approach requires tools to quickly retrieve comprehensive information about a genomic region and analyze the potential effects of coding and non-coding SNPs in a candidate gene region. Furthermore, once a candidate region is chosen for resequencing and fine-mapping studies, the identification of several rare mutations is likely and requires strong bioinformatic support to properly evaluate and prioritize the found mutations for further analysis. Due to the variety of regulatory layers that can be affected by a mutation, a comprehensive in-silico evaluation of candidate SNPs can be a demanding and very time-consuming task. Although many bioinformatic tools that significantly simplify this task were made available in the last years, their utility is often still unknown to researches not intensively involved in bioinformatics. We present a comprehensive guide of 64 tools and databases to bioinformatically analyze gene regions of interest to predict SNP effects. In addition, we discuss tools to perform data mining of large genetic regions, predict the presence of regulatory elements, make in-silico evaluations of SNPs effects and address issues ranging from interactome analysis to graphically annotated proteins sequences. Finally, we exemplify the use of these tools by applying them to hits of a recently performed GWAS. Taken together a combination of the discussed tools are summarized and constantly updated in the web-based "GenEpi Toolbox" (http://genepi_toolbox.i-med.ac.at) and can help to get a glimpse at the potential functional relevance of both large genetic regions and single nucleotide mutations which might help to prioritize the next steps.
DENG You-ping; AI Jun-mei; XIAO Pei-gen
One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds.Genome wide high throughput technologies such as genomics,transcriptomics,proteomics and metabolomics can help reach that goal.Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process,manage,distribute and understand these data.By dealing with the"omics"data,bioinformatics and systems biology can also help improve the quality of traditional medicinal materials,develop new approaches for the classification and authentication of medicinal plants,identify new active compounds,and cultivate medicinal plant species that tolerate harsh environmental conditions.In this review,the application of bioinformatics and systems biology in medicinal plants is briefly introduced.
João Carlos Sousa
Full Text Available The ability to manage the constantly growing information in genetics availableon the internet is becoming crucial in biochemical education and medicalpractice. Therefore, developing students skills in working with bioinformaticstools is a challenge to undergraduate courses in the molecular life sciences.The regulation of gene transcription by hormones and vitamins is a complextopic that influences all body systems. We describe a student centered activityused in a multidisciplinary “Functional Organ System“ course on the EndocrineSystem. By receiving, as teams, a nucleotide sequence of a hormone orvitamin-response element, students navigate through internet databases to findthe gene to which it belongs. Subsequently, student’s search how thecorresponding hormone/vitamin influences the expression of that particulargene and how a dysfunctional interaction might cause disease. This activity,proposed for 4 consecutive years to cohorts of 50-60 students/year enrolled inthe 2nd year our undergraduate medical degree, revealed that 90% of thestudents developed a better understanding of the usefulness of bioinformaticsand that 98% intend to use them in the future. Since hormones and vitaminsregulate genes of all body organ systems, this web-based activity successfullyintegrates the whole body physiology of the medical curriculum and can be ofrelevance to other courses on molecular life sciences.
Vears, R E
Microprocessor Interfacing provides the coverage of the Business and Technician Education Council level NIII unit in Microprocessor Interfacing (syllabus U86/335). Composed of seven chapters, the book explains the foundation in microprocessor interfacing techniques in hardware and software that can be used for problem identification and solving. The book focuses on the 6502, Z80, and 6800/02 microprocessor families. The technique starts with signal conditioning, filtering, and cleaning before the signal can be processed. The signal conversion, from analog to digital or vice versa, is expl
Fairbairn David J
Full Text Available Abstract Background A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. Description PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. Conclusion The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.
Full Text Available Quantitative proteomics applications in mass spectrometry depend on the knowledge of the mass-to-charge ratio (m/z values of proteotypic peptides for the proteins under study and their product ions. MRMPath and MRMutation, web-based bioinformatics software that are platform independent, facilitate the recovery of this information by biologists. MRMPath utilizes publicly available information related to biological pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG database. All the proteins involved in pathways of interest are recovered and processed in silico to extract information relevant to quantitative mass spectrometry analysis. Peptides may also be subjected to automated BLAST analysis to determine whether they are proteotypic. MRMutation catalogs and makes available, following processing, known (mutant variants of proteins from the current UniProtKB database. All these results, available via the web from well-maintained, public databases, are written to an Excel spreadsheet, which the user can download and save. MRMPath and MRMutation can be freely accessed. As a system that seeks to allow two or more resources to interoperate, MRMPath represents an advance in bioinformatics tool development. As a practical matter, the MRMPath automated approach represents significant time savings to researchers.
Rocco, D; Liu, L; Critchlow, T
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 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 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.
Approaches in Integrative Bioinformatics provides a basic introduction to biological information systems, as well as guidance for the computational analysis of systems biology. This book also covers a range of issues and methods that reveal the multitude of omics data integration types and the relevance that integrative bioinformatics has today. Topics include biological data integration and manipulation, modeling and simulation of metabolic networks, transcriptomics and phenomics, and virtual cell approaches, as well as a number of applications of network biology. It helps to illustrat
Manning, Timmy; Sleator, Roy D; Walsh, Paul
For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.
Phillips, J. C.
Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.
Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics and molecular modeling. The second part focuses on the use of multithreading for
Full Text Available This study presents a usability testing as method, which can be used to improve controlling of web map sites. Study refers to the basic principles of this method and describes particular usability tests of mapping sites. In this paper are identified potential usability problems of web sites: Amapy.cz, Google maps and Mapy.cz. The usability testing was focused on problems related with user interfaces, addresses searching and route planning of the map sites.
Ojo, O O; Omabe, M
The urgency to process and analyze the deluge of data created by proteomics and genomics studies worldwide has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. Several countries, in response to this challenge, have developed a number of manpower training programmes. This review presents a description of the meaning, scope, history and development of bioinformatics with focus on prospects and challenges facing bioinformatics education worldwide. The paper also provides an overview of attempts at the introduction of bioinformatics in Nigeria; describes the existing bioinformatics scenario in Nigeria and suggests strategies for effective bioinformatics education in Nigeria.
In the years since Jakob Nielsen's classic collection on interface consistency first appeared, much has changed, and much has stayed the same. On the one hand, there's been exponential growth in the opportunities for following or disregarding the principles of interface consistency-more computers, more applications, more users, and of course the vast expanse of the Web. On the other, there are the principles themselves, as persistent and as valuable as ever. In these contributed chapters, you'll find details on many methods for seeking and enforcing consistency, along with bottom-line analys
This article argues for seeing the interface as an important representational and aesthetic form with implications for postmodern culture and digital aesthetics. The interface emphasizes realism due in part to the desire for transparency in Human-Computer Interaction (HCI) and partly to the devel......This article argues for seeing the interface as an important representational and aesthetic form with implications for postmodern culture and digital aesthetics. The interface emphasizes realism due in part to the desire for transparency in Human-Computer Interaction (HCI) and partly...... to the development of illusionistic realism within computer graphics and games. The article compares the pragmatic realism of HCI with aesthetic notions of realism in the computer game Max Payne (illusionistic realism), the artist Jodi's game modifications (media realism), and Adrian Ward's software art work......, "Signwave Auto Illustrator" (functional realism)....
Goble, Carole A; Bhagat, Jiten; Aleksejevs, Sergejs; Cruickshank, Don; Michaelides, Danius; Newman, David; Borkum, Mark; Bechhofer, Sean; Roos, Marco; Li, Peter; De Roure, David
myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to email@example.com.
Mattmann, C. A.
Search has progressed through several stages due to the increasing size of the Web. Search engines first focused on text and its rate of occurrence; then focused on the notion of link analysis and citation then on interactivity and guided search; and now on the use of social media - who we interact with, what we comment on, and who we follow (and who follows us). The next stage, referred to as "deep search," requires solutions that can bring together text, images, video, importance, interactivity, and social media to solve this challenging problem. The Apache Nutch project provides an open framework for large-scale, targeted, vertical search with capabilities to support all past and potential future search engine foci. Nutch is a flexible infrastructure allowing open access to ranking; URL selection and filtering approaches, to the link graph generated from search, and Nutch has spawned entire sub communities including Apache Hadoop and Apache Tika. It addresses many current needs with the capability to support new technologies such as image and video. On the DARPA Memex project, we are creating create specific extensions to Nutch that will directly improve its overall technological superiority for search and that will directly allow us to address complex search problems including human trafficking. We are integrating state-of-the-art algorithms developed by Kitware for IARPA Aladdin combined with work by Harvard to provide image and video understanding support allowing automatic detection of people and things and massive deployment via Nutch. We are expanding Apache Tika for scene understanding, object/person detection and classification in images/video. We are delivering an interactive and visual interface for initiating Nutch crawls. The interface uses Python technologies to expose Nutch data and to provide a domain specific language for crawls. With the Bokeh visualization library the interface we are delivering simple interactive crawl visualization and
Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.
Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics
Graham, Matthew; Grid,
This document describes the minimum interface that a (SOAP- or REST-based) web service requires to participate in the IVOA. Note that this is not required of standard VO services developed prior to this specification, although uptake is strongly encouraged on any subsequent revision. All new standard VO services, however, must feature a VOSI-compliant interface. This document has been produced by the Grid and Web Services Working Group. It has been reviewed by IVOA Members and other interested parties, and has been endorsed by the IVOA Executive Committee as an IVOA Recommendation. It is a stable document and may be used as reference material or cited as a normative reference from another document. IVOA's role in making the Recommendation is to draw attention to the specification and to promote its widespread deployment. This enhances the functionality and interoperability inside the Astronomical Community.
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.
Bhattacharya, D.; M., M.
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.
Full Text Available 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.
Vu, Kim-Phuong L
The Handbook of Human Factors in Web Design covers basic human factors issues relating to screen design, input devices, and information organization and processing, as well as addresses newer features which will become prominent in the next generation of Web technologies. These include multimodal interfaces, wireless capabilities, and agents that can improve convenience and usability. Written by leading researchers and/or practitioners in the field, this volume reflects the varied backgrounds and interests of individuals involved in all aspects of human factors and Web design and includes chap
Get the latest information about using the #1 web analytics tool from this fully updated guide Google Analytics is the free tool used by millions of web site owners to assess the effectiveness of their efforts. Its revised interface and new features will offer even more ways to increase the value of your web site, and this book will teach you how to use each one to best advantage. Featuring new content based on reader and client requests, the book helps you implement new methods and concepts, track social and mobile visitors, use the new multichannel funnel reporting features, understand which
Campbell, Moray J
Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity. Integrative approaches can combine VDR ChIP-Seq in cell systems where significant volumes of publically available data are available. For example, VDR ChIP-Seq studies can be combined with genome-wide association studies to reveal significant associations to immune phenotypes. Similarly, VDR ChIP-Seq can be combined with data from Cancer Genome Atlas (TCGA) to infer the impact of VDR target genes in cancer progression. Therefore, bioinformatic approaches can reveal what aspects of VDR downstream networks are significantly related to disease or phenotype.
Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas
The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation.
McEntire, R; Karp, P; Abernethy, N; Benton, D; Helt, G; DeJongh, M; Kent, R; Kosky, A; Lewis, S; Hodnett, D; Neumann, E; Olken, F; Pathak, D; Tarczy-Hornoch, P; Toldo, L; Topaloglou, T
Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they satisfied each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusion of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua.
well as that are incorporated into InterPro (Mulder, et al., 2005). other users’ work. PUMA2 ( Maltsev , et al., 2006) incorporates more than 20 0-7695...pipeline for protocol-based bioinformatics analysis." Genome Res., 13(8), pp. 1904-1915, 2003. Maltsev , N. and E. Glass, et al., "PUMA2--grid-based 4
A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...
Forman, Michele R; Greene, Sarah M; Avis, Nancy E; Taplin, Stephen H; Courtney, Paul; Schad, Peter A; Hesse, Bradford W; Winn, Deborah M
Population science and disease control researchers can benefit from a more proactive approach to applying bioinformatics tools for clinical and public health research. Bioinformatics utilizes principles of information sciences and technologies to transform vast, diverse, and complex life sciences data into a more coherent format for wider application. Bioinformatics provides the means to collect and process data, enhance data standardization and harmonization for scientific discovery, and merge disparate data sources. Achieving interoperability (i.e. the development of an informatics system that provides access to and use of data from different systems) will facilitate scientific explorations and careers and opportunities for interventions in population health. The National Cancer Institute's (NCI's) interoperable Cancer Biomedical Informatics Grid (caBIG) is one of a number of illustrative tools in this report that are being mined by population scientists. Tools are not all that is needed for progress. Challenges persist, including a lack of common data standards, proprietary barriers to data access, and difficulties pooling data from studies. Population scientists and informaticists are developing promising and innovative solutions to these barriers. The purpose of this paper is to describe how the application of bioinformatics systems can accelerate population health research across the continuum from prevention to detection, diagnosis, treatment, and outcome.
Goto, N.; Prins, J.C.P.; Nakao, M.; Bonnal, R.; Aerts, J.; Katayama, A.
The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it suppor
Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki
The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it suppor
Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter
We have developed "GLYCANthrope " - CROSSWORKS for glycans: a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...
Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul
Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…
Lima, Andre O. S.; Garces, Sergio P. S.
Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…
The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering C...
Jungck, John R; Weisstein, Anton E
The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.
with a function of propelling or steering the evolution of a gene, phenotypic trait or species (Prakash 2008). Bioinformatics Research, development...platforms like SJOne. Ebola Viruses There are five known species of Ebola virus: Bundibugyo, Cote d’Ivoire, Reston, Sudan and Zaire. The relative
As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.
Geoffrey Webb Prof James Whisstock Dr Jianging Song Mr Khalid Mahmood Mr Cyril Reboul Ms Wan Ting Kan Publications: List peer-reviewed...Khalid Mahmood, Jianging Song, Cyril Reboul , Wan Ting Kan, Geoffrey I. Webb and James C. Whisstock. To be submitted to BMC Bioinformatics. Outline
Weisstein, Anton E.
The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621
The second, called the deep web , consists of roughly 96% or the rest of the web . The deep web consists of protected sites that re- quire users to...financial records, research & development), and personal data (medical records or legal documents). These are all deep web . Standard search engines...don’t have access to these sites and therefore cannot search them. The last web is the dark web , a part of the deep web . It requires specific software
Roby, W.; Wu, X.; Goldina, T.; Joliet, E.; Ly, L.; Mi, W.; Wang, C.; Zhang, Lijun; Ciardi, D.; Dubois-Felsmann, G.
At IPAC/Caltech, we have developed the Firefly web archive and visualization system. Used in production for the last eight years in many missions, Firefly gives the scientist significant capabilities to study data. Firefly provided the first completely web based FITS viewer as well as a growing set of tabular and plotting visualizers. Further, it will be used for the science user interface of the LSST telescope which goes online in 2021. Firefly must meet the needs of archive access and visualization for the 2021 LSST telescope and must serve astronomers beyond the year 2030. Recently, our team has faced the fact that the technology behind Firefly software was becoming obsolete. We were searching for ways to utilize the current breakthroughs in maintaining stability, testability, speed, and reliability of large web applications, which Firefly exemplifies. In the last year, we have ported the Firefly to cutting edge web technologies. Embarking on this massive overhaul is no small feat to say the least. Choosing the technologies that will maintain a forward trajectory in a future development project is always hard and often overwhelming. When a team must port 150,000 lines of code for a production-level product there is little room to make poor choices. This paper will give an overview of the most modern web technologies and lessons learned in our conversion from GWT based system to React/Redux based system.
... Initiative: Customer Relationship Management. Component: DHS Wide. Date of approval: December 10, 2009. The... Intergovernmental Affairs, are developing the Customer Relationship Management (CRM), a data management tool being... Management Information System Web Version Interface and Collection Update. Component: Immigration and......