The left pane of the application will host a tree structure that organizes all the data that you have imported and generated (1). Examples of objects in this tree are studies, genotype matrices, reports, charts and sample-info tables. Every time you select a given node of the above type in the tree, a context specific right side panel (2) will be shown to you. In the case above, the introduction screen, there is a list of help topics that are accessible to you via double-click.

The preferences button located at the bottom (3) will allow you to change the work folder your data will be stored under.