Eclipse runtime for plug-ins management

BioUML architecture uses Eclipse platform to provide BioUML workbench extensibility as well as seamless integration with other tools for systems biology. 

BioUML workbench is a plugin-based application framework. It consists from a core runtime kernel that supports 'plug-ins' and a set of plug-ins that support database access, diagram editing, and simulation for different complex systems.

A plug-in is a structured component that describes itself to the system using a XML-based manifest file (plugin.xml).  We use Eclipse runtime to start the workbench and dynamically discover plug-ins. The platform maintains a registry of installed plug-ins and the function they provide.

Functionality is added to BioUML workbench using a common extension model.

Extension points are well-defined function points in the system that can be extended by plug-ins. When a plug-in contributes an implementation for an extension point, we say that it adds an extension to the platform. Plug-ins can define their own extension points, so that other plug-ins can integrate tightly with them.

The extension mechanisms is the most basic means of adding function to the platform and other plug-ins.