The Experts below are selected from a list of 204 Experts worldwide ranked by ideXlab platform

Tetsuro Toyoda - One of the best experts on this subject based on the ideXlab platform.

  • semantic json a lightweight Web Service Interface for semantic Web contents integrating multiple life science databases
    Nucleic Acids Research, 2011
    Co-Authors: Norio Kobayashi, Manabu Ishii, Satoshi Takahashi, Yoshiki Mochizuki, Akihiro Matsushima, Tetsuro Toyoda
    Abstract:

    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.

Alejandro Zunino - One of the best experts on this subject based on the ideXlab platform.

  • keeping Web Service Interface complexity low using an oo metric based early approach
    2016 XLII Latin American Computing Conference (CLEI), 2016
    Co-Authors: Cristian Mateos, Alejandro Zunino, Sanjay Misra, Diego Anabalon, Andres Flores
    Abstract:

    Web Services have been steadily gaining maturity as their adoption in the software industry grew. Accordingly, metric suites for assessing different quality attributes of Web Service artifacts have been proposed recently. Some researchers have particularly focused on assessing Service Interface descriptions in WSDL, which like any other software artifact have several inherent attributes (e.g., size or complexity) that can be measured. We study the statistical relationships between some recent Service Interface complexity metrics (Basci & Misra's metrics suite) and the well-known Chidamber & Kemerer's metric suite applied to Service implementations, on a data-set of 154 real-world Services. First, to prove the ability of Basci & Misra's suite of measuring the complexity attribute in WSDL documents, a theoretical validation of these metrics using Weyuker's properties is presented. Then, after finding high correlation between both metric suites, we show that refactoring Service codes prior to generating the WSDL documents might reduce Service Interface complexity.

  • estimating Web Service Interface quality through conventional object oriented metrics
    Clei Electronic Journal, 2013
    Co-Authors: Jose Luis Ordiales Coscia, Marco Crasso, Cristian Mateos, Alejandro Zunino
    Abstract:

    Historically, software engineers have conceived metric suites as valuable tools to estimate the quality of their software artifacts. Recently, a fresh computing paradigm called Service-Oriented Computing (SOC) has emerged at the crossing of massively distributed and heterogeneous software. This paper presents a statistical correlation analysis showing that classic software engineering metrics can be used to predict the most relevant quality attributes of WSDL documents, the essential software artifact when materializing this novel computing paradigmwithWeb-based technologies. For the experiments, two recent WSDL-level metrics catalogs and 154 real world WSDL documents have been employed.

  • estimating Web Service Interface complexity and quality through conventional object oriented metrics
    Conferencia Iberoamericana de Software Engineering, 2012
    Co-Authors: Jose Luis Ordiales Coscia, Marco Crasso, Cristian Mateos, Alejandro Zunino
    Abstract:

    Historically, software engineers have conceived metric suites as valuable tools to estimate the quality of their software artifacts. Recently, a fresh computing paradigm called Service-Oriented Computing (SOC) has emerged at the crossing of massively distributed and heterogeneous software. This paper presents a statistical correlation analysis showing that classic software engineering metrics can be used to predict the complexity and quality of WSDL documents, the cornerstone software artifact when materializing this novel computing paradigm with Web-based technologies. For the experiments, 154 real world WSDL documents have been employed.

Steve Pettifer - One of the best experts on this subject based on the ideXlab platform.

  • biocatalogue a universal catalogue of Web Services for the life sciences
    Nucleic Acids Research, 2010
    Co-Authors: Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer
    Abstract:

    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.

Flanagan, Keith Stanley - One of the best experts on this subject based on the ideXlab platform.

  • A grid and cloud-based framework for high throughput bioinformatics
    2010
    Co-Authors: Flanagan, Keith Stanley
    Abstract:

    Recent advances in genome sequencing technologies have unleashed a flood of new data. As a result, the computational analysis of bioinformatics data sets has been rapidly moving from a labbased desktop computer environment to exhaustive analyses performed by large dedicated computing resources. Traditionally, large computational problems have been performed on dedicated clusters of high performance machines that are typically local to, and owned by, a particular institution. The current trend in Grid computing has seen institutions pooling their computational resources in order to offload excess computational work to remote locations during busy periods. In the last year or so, commercial Cloud computing initiatives have matured enough to offer a viable remote source of reliable computational power. Collections of idle desktop computers have also been used as a source of computational power in the form of ‘volunteer Grids’. The field of bioinformatics is highly dynamic, with new or updated versions of software tools and databases continually being developed. Several different tools and datasets must often be combined into a coherent, automated workflow or pipeline. While existing solutions are available for constructing workflows, there is a clear need for long-lived analyses consisting of many interconnected steps to be able to migrate among Grid and cloud computational resources dynamically. This project involved research into the principles underlying the design and architecture of flexible, high-throughput bioinformatics processes. Following extensive research into requirements gathering, a novel Grid-based platform, Microbase, has been implemented that is based on Service-oriented architectures and peer-to-peer data transfer technology. This platform has been shown to be amenable to utilising a wide range of hardware from commodity desktop computers, to high-performance cloud infrastructure. The system has been shown to drastically reduce the bandwidth requirements of bioinformatics data distribution, and therefore reduces both the financial and computational costs associated with cloud computing. The system is inherently modular in nature, comprising a Service based notification system, a data storage system scheduler and a job manager. In keeping with e-Science principles, each module can operate in physical isolation from each other, distributed within an intranet or Internet. Moreover, since each module is loosely coupled via Web Services, modules have the potential to be used in combination with external Service oriented components or in isolation as part of another system. In order to demonstrate the utility of such an open source system to the bioinformatics community, a pipeline of inter-connected bioinformatics applications was developed using the Microbase system to form a high throughput application for the comparative and visual analysis of microbial genomes. This application, Automated Genome Analyser (AGA) has been developed to operate without user interaction. AGA exposes its results via Web-Services which can be used by further analytical stages within Microbase, by external computational resources via a Web Service Interface or which can be queried by users via an interactive genome browser. In addition to providing the necessary infrastructure for scalable Grid applications, a modular development framework has been provided, which simplifies the process of writing Grid applications. Microbase has been adopted by a number of projects ranging from comparative genomics to synthetic biology simulations.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

  • A grid and cloud-based framework for high throughput bioinformatics
    Newcastle University, 2010
    Co-Authors: Flanagan, Keith Stanley
    Abstract:

    PhD ThesisRecent advances in genome sequencing technologies have unleashed a flood of new data. As a result, the computational analysis of bioinformatics data sets has been rapidly moving from a labbased desktop computer environment to exhaustive analyses performed by large dedicated computing resources. Traditionally, large computational problems have been performed on dedicated clusters of high performance machines that are typically local to, and owned by, a particular institution. The current trend in Grid computing has seen institutions pooling their computational resources in order to offload excess computational work to remote locations during busy periods. In the last year or so, commercial Cloud computing initiatives have matured enough to offer a viable remote source of reliable computational power. Collections of idle desktop computers have also been used as a source of computational power in the form of ‘volunteer Grids’. The field of bioinformatics is highly dynamic, with new or updated versions of software tools and databases continually being developed. Several different tools and datasets must often be combined into a coherent, automated workflow or pipeline. While existing solutions are available for constructing workflows, there is a clear need for long-lived analyses consisting of many interconnected steps to be able to migrate among Grid and cloud computational resources dynamically. This project involved research into the principles underlying the design and architecture of flexible, high-throughput bioinformatics processes. Following extensive research into requirements gathering, a novel Grid-based platform, Microbase, has been implemented that is based on Service-oriented architectures and peer-to-peer data transfer technology. This platform has been shown to be amenable to utilising a wide range of hardware from commodity desktop computers, to high-performance cloud infrastructure. The system has been shown to drastically reduce the bandwidth requirements of bioinformatics data distribution, and therefore reduces both the financial and computational costs associated with cloud computing. The system is inherently modular in nature, comprising a Service based notification system, a data storage system scheduler and a job manager. In keeping with e-Science principles, each module can operate in physical isolation from each other, distributed within an intranet or Internet. Moreover, since each module is loosely coupled via Web Services, modules have the potential to be used in combination with external Service oriented components or in isolation as part of another system. In order to demonstrate the utility of such an open source system to the bioinformatics community, a pipeline of inter-connected bioinformatics applications was developed using the Microbase system to form a high throughput application for the comparative and visual analysis of microbial genomes. This application, Automated Genome Analyser (AGA) has been developed to operate without user interaction. AGA exposes its results via Web-Services which can be used by further analytical stages within Microbase, by external computational resources via a Web Service Interface or which can be queried by users via an interactive genome browser. In addition to providing the necessary infrastructure for scalable Grid applications, a modular development framework has been provided, which simplifies the process of writing Grid applications. Microbase has been adopted by a number of projects ranging from comparative genomics to synthetic biology simulations

Roger Villemaire - One of the best experts on this subject based on the ideXlab platform.

  • runtime verification of Web Service Interface contracts
    IEEE Computer, 2010
    Co-Authors: Sylvain Hallé, Tevfik Bultan, Graham Hughes, Muath Alkhalaf, Roger Villemaire
    Abstract:

    Asynchronous JavaScript and XML (Ajax) is a collection of technologies used to develop rich and interactive Web applications. A typical Ajax client runs locally in the user's Web browser and refreshes its Interface on the fly in response to user input. Using this method with the AWS-ECS let us automatically generate test sequences and detect two deviations of their Service implementation with respect to the online documentation provided, in less than three minutes of testing. We also provided a framework that allows the runtime monitoring of both client and server contract constraints with minimal modification to an existing Ajax application code. Experiments with the Amazon E-Commerce Service demonstrate the advantages of using a model-based approach for the runtime testing and monitoring of Web applications.

  • model based runtime verification of Web Service Interface contracts
    IEEE Computer, 2009
    Co-Authors: Sylvain Hallé, Tevfik Bultan, Graham Hughes, Muath Alkhalaf, Roger Villemaire
    Abstract:

    Web applications are required to follow an Interface contract that specifies their expected behaviour when they communicate with a Web Service. Using the Amazon E-­Commerce Service as an example, we show how we can automatically test an implementation for conformance as well as monitor at runtime that each partner fulfills its part of the contract.