TY - JOUR
T1 - KBWS
T2 - An EMBOSS associated package for accessing bioinformatics web services
AU - Oshita, Kazuki
AU - Arakawa, Kazuharu
AU - Tomita, Masaru
N1 - Funding Information:
We would like to thank Nobuaki Kono and Keita Ikegami for technical advices. This research was supported by the Grant-in-Aid for Young Scientists No.222681029 from the Japan Society for the Promotion of Science (JSPS), and by funds from the Yamagata Prefectural Government and Tsuruoka City.
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).
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U2 - 10.1186/1751-0473-6-8
DO - 10.1186/1751-0473-6-8
M3 - Article
C2 - 21529350
AN - SCOPUS:79955400512
SN - 1751-0473
VL - 6
JO - Source Code for Biology and Medicine
JF - Source Code for Biology and Medicine
M1 - 8
ER -