KBWS: an EMBOSS associated package for accessing bioinformatics web services
Open Access
- 29 April 2011
- journal article
- Published by Springer Science and Business Media LLC in Source Code for Biology and Medicine
- Vol. 6 (1), 8
- https://doi.org/10.1186/1751-0473-6-8
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).Keywords
This publication has 14 references indexed in Scilit:
- MOWServ: a web client for integration of bioinformatic resourcesNucleic Acids Research, 2010
- BioCatalogue: a universal catalogue of web services for the life sciencesNucleic Acids Research, 2010
- The case for cloud computing in genome informaticsGenome Biology, 2010
- jORCA: easily integrating bioinformatics Web ServicesBioinformatics, 2010
- Towards a cyberinfrastructure for the biological sciences: progress, visions and challengesNature Reviews Genetics, 2008
- Experience using web services for biological sequence analysisBriefings in Bioinformatics, 2008
- Interoperability with Moby 1.0--It's better than sharing your toothbrush!Briefings in Bioinformatics, 2008
- Seahawk: moving beyond HTML in Web-based bioinformatics analysisBMC Bioinformatics, 2007
- Taverna: a tool for the composition and enactment of bioinformatics workflowsBioinformatics, 2004
- EMBOSS: The European Molecular Biology Open Software SuiteTrends in Genetics, 2000