The Sci2 Tool is an 'empty shell' filled with plugins. Some plugins run on the core architecture, OSGi and CIShell (see Section 7. Extending the Sci2 Tool). Others convert loaded data into in-memory objects, formatted for different algorithms to read it. The algorithm plugins themselves can be divided into different menus, in this case data preparation, preprocessing, analysis, modeling and visualization. Users are not limited to using pre-packaged plugins; instead, they can create, download, share, and import their own.
There are two ways plugins can be added to the menu. First, if an algorithm is listed in the default_menu.xml file, which is found in the configuration/ directory of a CIShell tool, it is added in the place specified by the default_menu.xml file. Secondly, if an algorithm is not listed in this file, but has specified a menu_path property in the algorithm.properties file, the menu manager CIShell service will add it to the appropriate menu, as described in the by the menu_path property's value (for example, Analysis/additions will place an algorithm on the bottom of the Analysis menu).
It is possible to extend Sci2 Tool, by adding plugins related to database functionalities and Cytoscape tool (open source software platform for visualizing networks).