Articlehybrid2010

jORCA: easily integrating bioinformatics Web Services

Victoria Martín-Requena · Javier Ríos · Sergio Ramírez · Oswaldo Trelles

25 citations0/0 files storedBioinformatics

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Scientific Computing and Data Management Service-Oriented Architecture and Web Services Genetics, Bioinformatics, and Biomedical Research

Abstract

Abstract Motivation: Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats—and this presents a barrier to service interoperability. Results: jORCA is a desktop client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users. Availability and Implementation: jORCA binaries and extended documentation are freely available at http://www.bitlab-es.com/jorca under the Creative Commons Attribution-No Derivative Works 2.5 Spain License and jORCA source code (implemented in Java) is available under request. (GPL v3 license). jORCA has been tested under UNIX (Fedora 11, open SUSE 11 and Ubuntu 8.1), MS-Windows and Mac OS 10.5 operating systems. Java VM version 1.6.0 later is required. Contact: ots@uma.es or vickymr@uma.es Supplementary information: Supplementary data are available at Bioinformatics online.

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References

2004Taverna: a tool for the composition and enactment of bioinformatics workflows 2008Interoperability With Moby 1.0 - It's Better Than Sharing Your Toothbrush!2007The myGrid ontology: bioinformatics service discovery 2007Seahawk: moving beyond HTML in Web-based bioinformatics analysis 2006REMORA: a pilot in the ocean of BioMoby web-services 2005Intelligent client for integrating bioinformatics services 2009Magallanes: a web services discovery and automatic workflow composition tool 2009BioCatalogue: A Curated Web Service Registry For The Life Science Community

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