Open source apis for processing the XML result of web services

An increasing number of web services providing convenient access to seismological data have become available in recent years. A huge effort at multiple levels was required to achieve this goal and the seismological community was engaged in the standardization of both data formats and web services. Although access to seismological data is much easier than in the past, users encounter problems because of the large number of web services, and due to the complexity of the discipline-specific data encodings. In addition, instead of adopting cross-disciplinary standards such as those by the Open Geospatial Consortium (OGC), most seismological web services created their own standards, primarily those by the International Federation of Digital Seismograph Networks (FDSN). This article introduces “QQuake,” a plugin for QGIS—the Open Source Geographic Information System—that aims at making access to seismological data easier. The plugin is based on an Open Source code available on GitHub, and it is designed in a modular and customizable way, allowing users to easily include new web services.

Download Full-text

Design and Managing of Distributed Virtual Organizations

Virtual Communities ◽

10.4018/978-1-60960-100-3.ch206 ◽

2011 ◽

pp. 463-468

Author(s):

Diego Liberati

Keyword(s):

Web Services ◽

Open Source ◽

Virtual Organizations ◽

Organizational Dynamics ◽

Service Invocation ◽

Cooperative Enterprise ◽

Open Source Systems ◽

Public Environment

A framework is proposed that creates, uses, communicates, and distributes information whose organizational dynamics allow it to perform a distributed cooperative enterprise in public environments even over open source systems. The approach assumes Web services as the enacting paradigm, possibly over a grid, to formalize interaction as cooperative services on various computational nodes of a network. A framework is thus proposed that defines the responsibility of e-nodes in offering services and the set of rules under which each service can be accessed by e-nodes through service invocation. By discussing a case study, the chapter will detail how specific classes of interactions can be mapped into a serviceoriented model whose implementation will be carried out in a prototypical public environment.

Download Full-text

Extending Apache Axis for Monitoring of Web Service Offerings

Electronic Commerce ◽

10.4018/978-1-59904-943-4.ch053 ◽

2011 ◽

pp. 641-658

Author(s):

Vladimir Tosic ◽

Wei Ma ◽

Babak Pagurek ◽

Bernard Pagurek ◽

Hanan Lutfiyya

Keyword(s):

Web Services ◽

Web Service ◽

Open Source ◽

Case Studies ◽

Management Information ◽

Prototype Implementation ◽

Service Deployment ◽

Technical Details ◽

Service Offering ◽

The Web

The Web Service Offerings Infrastructure (WSOI) is a monitoring and management infrastructure for the Web Service Offerings Language (WSOL). It extends Apache Axis, an open-source tool for hosting Web services. We present technical details of several WSOI solutions for monitoring Web Services. To pass management information among management parties, we built WSOI serializer and WSOI deserializer modules converting data between formats of Axis’ MessageContext properties and SOAP headers. To perform different monitoring activities for different WSOL service offerings, we implemented Web Service Offering Descriptor (WSOD) as a complement to Axis’ Web Service Deployment Descriptor (WSDD) component. To represent run-time values of WSOL-related management information, we developed WSOI management information model. All these solutions were verified with a prototype implementation of WSOI 2.0 and validated on case studies.

Download Full-text

Extending Apache Axis for Monitoring of Web Service Offerings

Global Information Technologies ◽

10.4018/978-1-59904-939-7.ch072 ◽

2008 ◽

pp. 944-960

Author(s):

Vladimir Tosic ◽

Wei Ma ◽

Babak Esfandiari ◽

Bernard Pagurek ◽

Hanan Lutfiyya

Keyword(s):

Web Services ◽

Web Service ◽

Open Source ◽

Case Studies ◽

Management Information ◽

Prototype Implementation ◽

Service Deployment ◽

Technical Details ◽

Service Offering ◽

The Web

The Web Service Offerings Infrastructure (WSOI) is a monitoring and management infrastructure for the Web Service Offerings Language (WSOL). It extends Apache Axis, an open-source tool for hosting Web services. We present technical details of several WSOI solutions for monitoring Web Services. To pass management information among management parties, we built WSOI serializer and WSOI deserializer modules converting data between formats of Axis’ MessageContext properties and SOAP headers. To perform different monitoring activities for different WSOL service offerings, we implemented Web Service Offering Descriptor (WSOD) as a complement to Axis’ Web Service Deployment Descriptor (WSDD) component. To represent run-time values of WSOL-related management information, we developed WSOI management information model. All these solutions were verified with a prototype implementation of WSOI 2.0 and validated on case studies.

Download Full-text

Design and Managing of Distributed Virtual Organizations

Handbook of Research on Virtual Workplaces and the New Nature of Business Practices ◽

10.4018/978-1-59904-893-2.ch040 ◽

2011 ◽

pp. 564-569

Author(s):

Diego Liberati

Keyword(s):

Web Services ◽

Open Source ◽

Virtual Organizations ◽

Organizational Dynamics ◽

Service Invocation ◽

Cooperative Enterprise ◽

Open Source Systems ◽

Public Environment

A framework is proposed that creates, uses, communicates, and distributes information whose organizational dynamics allow it to perform a distributed cooperative enterprise in public environments even over open source systems. The approach assumes Web services as the enacting paradigm, possibly over a grid, to formalize interaction as cooperative services on various computational nodes of a network. A framework is thus proposed that defines the responsibility of e-nodes in offering services and the set of rules under which each service can be accessed by e-nodes through service invocation. By discussing a case study, the chapter will detail how specific classes of interactions can be mapped into a serviceoriented model whose implementation will be carried out in a prototypical public environment.

Download Full-text

A Framework for Semantic Grid in E-Science

Handbook of Research on Grid Technologies and Utility Computing ◽

10.4018/978-1-60566-184-1.ch023 ◽

2009 ◽

pp. 235-240

Author(s):

Diego Liberati

Keyword(s):

Web Services ◽

Open Source ◽

Organizational Dynamics ◽

Semantic Grid ◽

Collaborative Environment ◽

Cooperative Enterprise ◽

Open Source Systems ◽

The Web ◽

Generally True

A framework is proposed that creates, uses, and communicates information, whose organizational dynamics allows performing a distributed cooperative enterprise in public environments, even over open source systems. The approach assumes the web services as the enacting paradigm possibly over a grid, to formalize interactions as cooperative services on various computational nodes of a network. The illustrated case study shows that some portions, both of processes and of data or knowledge, can be shared in a collaborative environment, which is also more generally true for any kind of either complex or resource demanding (or both) interaction that will benefit any of the approaches.

Download Full-text

BioMOBY: An open source biological web services proposal

Briefings in Bioinformatics ◽

10.1093/bib/3.4.331 ◽

2002 ◽

Vol 3 (4) ◽

pp. 331-341 ◽

Cited By ~ 190

Author(s):

M. D. Wilkinson

Keyword(s):

Web Services ◽

Open Source

Download Full-text

Interactive Access to LP DAAC Satellite Data Archives Through a Combination of Open-Source and Custom Middleware Web Services

IEEE Geoscience and Remote Sensing Magazine ◽

10.1109/mgrs.2015.2505999 ◽

2015 ◽

Vol 3 (4) ◽

pp. 8-20 ◽

Cited By ~ 1

Author(s):

Brian N. Davis ◽

Jason Werpy ◽

Aaron Friesz ◽

Kevin Impecoven ◽

Robert L. Quenzer ◽

...

Keyword(s):

Web Services ◽

Open Source ◽

Satellite Data ◽

Data Archives

Download Full-text

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

10.1101/019067 ◽

2015 ◽

Cited By ~ 5

Author(s):

Abhinav Nellore ◽

Leonardo Collado-Torres ◽

Andrew E Jaffe ◽

José Alquicira-Hernández ◽

Jacob Pritt ◽

...

Keyword(s):

Statistical Analysis ◽

Web Services ◽

Open Source ◽

Rna Sequencing ◽

Open Source Software ◽

Rna Seq ◽

Spliced Alignment ◽

Amazon Web Services ◽

Scalable Analysis ◽

Multiple Samples

RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it is difficult to reproduce the exact analysis without access to original computing resources. We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners. We use Rail-RNA to align 667 RNA-seq samples from the GEUVADIS project on Amazon Web Services in under 16 hours for US$0.91 per sample. Rail-RNA produces alignments and base-resolution bigWig coverage files, ready for use with downstream packages for reproducible statistical analysis. We identify expressed regions in the GEUVADIS samples and show that both annotated and unannotated (novel) expressed regions exhibit consistent patterns of variation across populations and with respect to known confounders. Rail-RNA is open-source software available at http://rail.bio.

Download Full-text

Converting Biomedical Text Annotated Resources into FAIR Research Objects with an Open Science Platform

Applied Sciences ◽

10.3390/app11209648 ◽

2021 ◽

Vol 11 (20) ◽

pp. 9648

Author(s):

Alexandros Kanterakis ◽

Nikos Kanakaris ◽

Manos Koutoulakis ◽

Konstantina Pitianou ◽

Nikos Karacapilidis ◽

...

Keyword(s):

Web Services ◽

Open Source ◽

Semantic Annotation ◽

Workflow Management ◽

Open Science ◽

Free Access ◽

Biomedical Text ◽

Text Annotation ◽

Text Corpora ◽

Research Objects

Today, there are excellent resources for the semantic annotation of biomedical text. These resources span from ontologies, tools for NLP, annotators, and web services. Most of these are available either in the form of open source components (i.e., MetaMap) or as web services that offer free access (i.e., Whatizit). In order to use these resources in automatic text annotation pipelines, researchers face significant technical challenges. For open-source tools, the challenges include the setting up of the computational environment, the resolution of dependencies, as well as the compilation and installation of the software. For web services, the challenge is implementing clients to undertake communication with the respective web APIs. Even resources that are available as Docker containers (i.e., NCBO annotator) require significant technical skills for installation and setup. This work deals with the task of creating ready-to-install and run Research Objects (ROs) for a large collection of components in biomedical text analysis. These components include (a) tools such as cTAKES, NOBLE Coder, MetaMap, NCBO annotator, BeCAS, and Neji; (b) ontologies from BioPortal, NCBI BioSystems, and Open Biomedical Ontologies; and (c) text corpora such as BC4GO, Mantra Gold Standard Corpus, and the COVID-19 Open Research Dataset. We make these resources available in OpenBio.eu, an open-science RO repository and workflow management system. All ROs can be searched, shared, edited, downloaded, commented on, and rated. We also demonstrate how one can easily connect these ROs to form a large variety of text annotation pipelines.

Download Full-text