Use diagram of integrating Taverna, Galaxy, and Tavaxy workflows. Tavaxy is a standalone workflow system that executes Tavaxy workflows as well as integrates and executes Taverna and Galaxy workflows. Galaxy workflows are compatible with Tavaxy and can be imported and executed directly on the system. For Taverna workflows, the integration can take place at either run-time or design-time. At run time, the Taverna (sub-) workflows can be executed as a whole by calling the Taverna engine. They can also be saved as sub-workflows and used within other Tavaxy workflows. At workflow design time, Taverna workflows are translated to the Tavaxy language, enabling them to be edited and enhanced. In this case, the user has the option of replacing any of the remote calls in the Taverna workflow with calls to equivalent local tools. Any remaining Taverna sub-workflow fragments can be directly executed using the Taverna engine. As an optimization, sub-workflows can be encapsulated into maximal external sub-workflows so as to minimize execution overheads. The implementation section addresses the maximal external sub-workflows in more details.