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KBWS: an EMBOSS associated package for accessing bioinformatics web servicesAbstract: With more than 1700 services listed in the BioCatalogue at the time of this writing [1], a significant number of biological resources and tools is provided as web-based services, in light of their advantages in interoperability, ease of use, and the lack of requirements for the compute infrastructure as well as the effort in installation and maintenance [2]. Several efforts have already utilized hundreds of these resources with the aim to effectively integrate them into a bioinformatics cyberinfrastructure, allowing the creation and management of research workflows through syntactic and semantic integration [3]. BioMoby project [4] maintains a repository of service descriptions with controlled vocabularies so that services can be discovered from their purpose and from their input/output data types, and MOWServ project [5] further classifies and curates the services in order to allow automatic workflow creation [6]. A number of clients with rich graphical user interface such as Seahawk [7] and Taverna [8] are also available as front-end research environment.While the advent of web-based services is expected to proliferate further especially in light of the introduction of next-generation sequencers and their huge masses of data [9], local tools will continue to be important for numerous purposes, and web-based services need to be integrated with these local tools. Therefore, here we present the Keio Bioinformatics Web Service (KBWS), a collection of proxy client tools for 42 major bioinformatics web-based services in the form of European Molecular Biology Open Software Suite (EMBOSS) [10] associated software (EMBASSY) package of UNIX command-line utilities. EMBOSS is one of the most widely used collection of more than 200 bioinformatics tools, which takes advantage of the UNIX environment for "piping" with any other UNIX commands. With its Ajax Command Definitions (ACD), EMBOSS is well curated with controlled vocabularies and semantics so that the tools are highly do
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