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JAva Bioinformatics Analysis Web Services projects background


The JAva Bioinformatics Analysis Web Services (JABAWS) framework enables programs like Jalview to access bioinformatics analysis tools via SOAP web services. Unlike most other web services models, JABAWS is designed for easy installation, and can be deployed by an individual on a workstation or a cluster with little or no coding or systems administration experience.


Jalview is one of the most widely used multiple sequence alignment editing, analysis and visualisation tools, with over 20,000 users worldwide. It provides integrated tree, structure and annotation views and calls SOAP and REST web services for compute intensive analyses. The majority of analysis services that Jalview accesses are provided by JABAWS.

JABAWS Development Process

The JAva Bioinformatics Analysis (JABA) framework provides the methods and parameter models needed for creating and managing the execution of command line bioinformatics analysis programs. Wrapped programs can then be exposed as SOAP services using standard tools, and the source and binaries incorporated into the JABAWS server, ready for distribution. Unit tests (via TestNG) are developed for each stage of the wrapping process, which enables anyone running JABAWS to easily test if a particular service is working correctly on their system.