Bioclipse concepts

The BioResource concept

A BioResource (=BioclipseResource) encompasses all resources that Bioclipse is able to handle. This includes (but is not limited to) molecules, spectra, sequences, proteins, scripts etc. A folder is also a BioResource. All non-recognized resourcecs are marked as UNKNOWN by Bioclipse. Please note that a BioResource has nothing to do with the Eclipse Resource concept.

Perspectives

Perspectives are collections of editors and views that are grouped into a page on screen, e.g. the Chemoinformatics perspective in Bioclipse displays views and editors for working with molecules.

Views

In SWT, a View is a window that provides some graphical interface to present something for a user, and might let him interact with it. Examples are the BioResource Navigator, the Jmol View and the properties view.

Editors

An Editor is focused on letting the user edit an underlying model and follows the load-save cycle. An example is a simple editor for text-files, but could also be more advanced such as a graphical objects editor like the JchemPaint editor.

Plugins

Bioclipse (and Eclipse in general) is completely made up of plugins. The core of Bioclipse is itself a plugin with the most basic functionality, standard views, and editors. The rest of the functionality is contributed via plugins. For example does the bc_jmol plugin contribute a 3D-visualization based on Jmol, bc_cdk provides molecular management and analysis using the CDK libraries etc. This means that a certain plugin must be installed in order for its functionality to be available for the user. This is powerful in many ways; A user may select to run only the desired plugins and not clutter the workbench with unused functionality, and developers have a perfect framework for plugging in their own extensions to Bioclipse and not interfere with other.