[2][3] Biclipse gained scripting functionality in 2009,[4] and a command line version in 2021.

[5] Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality.

It extends the scripting language with managers that wrap the functionality of third party libraries, as mentioned above.

These scripts thus provide means to make analyses in Bioclipse sharable, for example, on MyExperiment.org.