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

Henrique Velloso, Ricardo A Vialle, J Miguel Ortega
2015 BMC Research Notes  
Conclusions: Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients.  ...  Results: Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters.  ...  Here we present bioinformatics open web services (BOWS), a web services platform that allows centralized and standardized access to bioinformatics tools.  ... 
doi:10.1186/s13104-015-1190-0 pmid:26032494 pmcid:PMC4467627 fatcat:be5yb5npjngk5nqoabx4vdldj4

IBWS: IST Bioinformatics Web Services

Achille Zappa, Mariangela Miele, Paolo Romano
2010 Nucleic Acids Research  
In order to make this information available through application programming interfaces, we implemented a suite of free web services (WS), called the 'IST Bioinformatics Web Services (IBWS)'.  ...  A support web site, including a description of the system, a list of available WS together with help pages, links to corresponding WSDLs and forms for testing services, is available at  ...  RESULTS Access to IST Bioinformatics Web Services A support web site, including a description of the system, and a list of available WS, together with help pages, links to corresponding WSDLs, examples  ... 
doi:10.1093/nar/gkq416 pmid:20484374 pmcid:PMC2896171 fatcat:gwzkmesjybhtdgv2xopus2ihgm

ballaxy: web services for structural bioinformatics

Anna Katharina Hildebrandt, Daniel Stöckel, Nina M. Fischer, Luis de la Garza, Jens Krüger, Stefan Nickels, Marc Röttig, Charlotta Schärfe, Marcel Schumann, Philipp Thiel, Hans-Peter Lenhof, Oliver Kohlbacher (+1 others)
2014 Computer applications in the biosciences : CABIOS  
Motivation: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics.  ...  Results: In this work, we address the problem of building a webbased system for workflows in structural bioinformatics.  ...  to the web service, and vice versa.  ... 
doi:10.1093/bioinformatics/btu574 pmid:25183489 fatcat:4hhq6drymrgrff3cadqkjaxasa

Evolution of web services in bioinformatics

P. B. T. Neerincx
2005 Briefings in Bioinformatics  
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  ...  To make SOAPbased web services just as successful as tools based on HTML interfaces, the bioinformatics community needs a web crawler to index web services similar to what Google is for web sites.  ... 
doi:10.1093/bib/6.2.178 pmid:15975226 fatcat:alotxt4xurbbxavufbwrm6k6my

DNA microarray technology and bioinformatic web services

Payam Behzadi, Reza Ranjbar
2018 Acta Microbiologica et Immunologica Hungarica  
The knowledge of bioinformatics plays a key role in association with probe designing and the utilization of correct probe sets and platforms.  ...  Wuju Li's sincere collaboration for introducing the web page of Mprobe 2.0: Computer-aided probe design for oligonucleotide microarrays (http://ccb.bmi.ac.cn:81/mprobe/).  ...  Our final goal in DNA microarray technology leads us to recruit proper online and/or offline tools, software, databases, and other web services.  ... 
doi:10.1556/030.65.2018.028 pmid:30010394 fatcat:62kkogabjbbdlfyoiesdygzc7y

Web Services at the European Bioinformatics Institute

A. Labarga, F. Valentin, M. Anderson, R. Lopez
2007 Nucleic Acids Research  
Results and discussion One of the main advantages of web services is that researches can construct easily bioinformatics workflows and pipelines combining two or more web services to solve complex biological  ...  Moreover, Web Services provide easier integration and interoperability between bioinformatics applications and the data they require.  ... 
doi:10.1093/nar/gkm291 pmid:17576686 pmcid:PMC1933145 fatcat:tc6mwelg3rbnpgqjfqr26v3y5i

BioSWR – Semantic Web Services Registry for Bioinformatics

Dmitry Repchevsky, Josep Ll. Gelpi, Yu Xue
2014 PLoS ONE  
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.  ...  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.  ...  registry for bioinformatics Web services.  ... 
doi:10.1371/journal.pone.0107889 pmid:25233118 pmcid:PMC4169436 fatcat:z7frhotehfguhcadxtyf4umava

An active registry for bioinformatics web services

S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, D. Mowbray, G. Vriend
2009 Bioinformatics  
The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators.  ...  Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks.  ...  INTRODUCTION 'Web services' have become important tools in bioinformatics, allowing databases and algorithms to be accessed programmatically as computational components in programs, workflows and interactive  ... 
doi:10.1093/bioinformatics/btp329 pmid:19460889 pmcid:PMC2722997 fatcat:flbwio7kzbdmbcct5jlitsrtqe

BioInfoWF – WEB SERVICES AND WEB INTERFACES GENERATOR FOR BIOINFORMATICS ANALYSIS

M. A. Genaev, E. G. Komyshev, K. V. Gunbin, D. A. Afonnikov
2014 Vavilovskij Žurnal Genetiki i Selekcii  
The BioinfoWF (Bioinformatics WorkFlow) system for automated generation of Web interface and Web services for bioinformatics programs.  ...  The metadescriptions are used for automated generation of Web interface and Web services that can be used further in bioinformatics workflows. Computational modules can be organized in workflows.  ...  и Web-сервисов.  ... 
doaj:25297d690d5d48049f94d335fd49ad72 fatcat:ggilidlujzbftimfvpliwegh3m

NGScloud2: optimized bioinformatic analysis using Amazon Web Services

Fernando Mora-Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
2021 PeerJ  
NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services.  ...  The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made  ...  CONCLUSIONS NGScloud2 has significantly expanded the types of bioinformatics workflows to run using Amazon Web Services since its previous version.  ... 
doi:10.7717/peerj.11237 pmid:33959420 pmcid:PMC8054753 fatcat:pb7gzj47rran5hpihifrz4lzga

WIWS: a protein structure bioinformatics Web service collection

M. L. Hekkelman, T. A. H. te Beek, S. R. Pettifer, D. Thorne, T. K. Attwood, G. Vriend
2010 Nucleic Acids Research  
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  ...  The web services run on a dedicated computational cluster; their function and availability is monitored daily.  ...  Acting as a subroutine or function that resides on a remote computer, web services provide a number of benefits to bioinformatics software developers (and thence directly or indirectly also to life scientist  ... 
doi:10.1093/nar/gkq453 pmid:20501602 pmcid:PMC2896166 fatcat:yrlsk3c5h5dvvkdctglkpud53u

Web services at the European Bioinformatics Institute-2009

H. Mcwilliam, F. Valentin, M. Goujon, W. Li, M. Narayanasamy, J. Martin, T. Miyar, R. Lopez
2009 Nucleic Acids Research  
From the user's point of view, these Web Services provide the same functionality as the browser-based forms.  ...  The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997.  ...  Many other providers of bioinformatic tools and databases have also adopted Web Services technologies.  ... 
doi:10.1093/nar/gkp302 pmid:19435877 pmcid:PMC2703973 fatcat:5kah2noaqjhjbd477rxenbrxvu

NGScloud2: optimized bioinformatic analysis using Amazon Web Services [article]

Fernando Mora-Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
2020 bioRxiv   pre-print
NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services.  ...  The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made  ...  Current Bioinformatics 15:420-430. DOI:  ... 
doi:10.1101/2020.11.30.400010 fatcat:wwscym3s4fekzordly5hmrx6b4

MAPI: towards the integrated exploitation of bioinformatics Web Services

Sergio Ramirez, Johan Karlsson, Oswaldo Trelles
2011 BMC Bioinformatics  
Bioinformatics is commonly featured as a well assorted list of available web resources.  ...  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.  ...  Acknowledgements This work has been partially supported by the National Institute of Bioinformatics (INB), Spain (a platform of the ISCIII) and the RIRAAF network (RD07/0064/0017).  ... 
doi:10.1186/1471-2105-12-419 pmid:22032807 pmcid:PMC3219744 fatcat:o5ux5w2imjhxpnprfvpuaxxwky

WAVES: a web application for versatile enhanced bioinformatic services

Marc Chakiachvili, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent Lefort, John Hancock
2018 Bioinformatics  
WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software.  ...  Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications.  ...  WAVES provides three different ways for users to access bioinformatic services. It creates "WEB PAGES" for direct user access via web browsers.  ... 
doi:10.1093/bioinformatics/bty639 pmid:30052762 fatcat:xlrnvvi6xzetzjo4uytw2soqda
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