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: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

BACKGROUND: To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes it difficult to find the right tool, or more importantly, the right set of tools that can work together to solve real complex problems. RESULTS: Magallanes (Magellan) is a versatile, platform-independent Java library of algorithms aimed at discovering bioinformatics web services and associated data types. A second important feature of Magallanes is its ability to connect available and compatible web services into workflows that can process data sequentially to reach a desired output given a particular input. Magallanes' capabilities can be exploited both as an API or directly accessed through a graphic user interface.The Magallanes' API is freely available for academic use, and together with Magallanes application has been tested in MS-Windows XP and Unix-like operating systems. Detailed implementation information, including user manuals and tutorials, is available at http://www.bitlab-es.com/magallanes. CONCLUSION: Different implementations of the same client (web page, desktop applications, web services, etc.) have been deployed and are currently in use in real installations such as the National Institute of Bioinformatics (Spain) and the ACGT-EU project. This shows the potential utility and versatility of the software library, including the integration of novel tools in the domain and with strong evidences in the line of facilitate the automatic discovering and composition of workflows.