KBWS: An EMBOSS associated package for accessing bioinformatics web services

Research output: Contribution to journalArticle

1 Citation (Scopus)

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).

Original languageEnglish
Article number8
JournalSource Code for Biology and Medicine
Volume6
DOIs
Publication statusPublished - 2011 Apr 29

Fingerprint

Molecular biology
Bioinformatics
Computational Biology
Web services
Molecular Biology
Software
Soaps
Language
Soaps (detergents)
Interoperability
WSDL
Secondary Protein Structure
UNIX
Workflow
Proxy
RNA
Semantics
World Wide Web
User interfaces
Sequence Analysis

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Information Systems and Management
  • Health Informatics

Cite this

@article{8884ebc589eb45a7bdaaa7ca6fbc234d,
title = "KBWS: An EMBOSS associated package for accessing bioinformatics web services",
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).",
author = "Kazuki Oshita and Kazuharu Arakawa and Masaru Tomita",
year = "2011",
month = "4",
day = "29",
doi = "10.1186/1751-0473-6-8",
language = "English",
volume = "6",
journal = "Source Code for Biology and Medicine",
issn = "1751-0473",
publisher = "BioMed Central",

}

TY - JOUR

T1 - KBWS

T2 - An EMBOSS associated package for accessing bioinformatics web services

AU - Oshita, Kazuki

AU - Arakawa, Kazuharu

AU - Tomita, Masaru

PY - 2011/4/29

Y1 - 2011/4/29

N2 - 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).

AB - 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).

UR - http://www.scopus.com/inward/record.url?scp=79955400512&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79955400512&partnerID=8YFLogxK

U2 - 10.1186/1751-0473-6-8

DO - 10.1186/1751-0473-6-8

M3 - Article

C2 - 21529350

AN - SCOPUS:79955400512

VL - 6

JO - Source Code for Biology and Medicine

JF - Source Code for Biology and Medicine

SN - 1751-0473

M1 - 8

ER -