Figure 2‑6 shows the AVA main window with its Project window in the front, showing the new (empty) Project. The ‘Project Name’ and ‘Location’ fields at the top left of the window match the new Project information we just entered. The ‘Project’ tab is in bold black lettering on blue background with a green square icon, indicating it is ready to be used to setup the Project. The other two accessible tabs are ‘Overview’ and ‘Computations’ (black type on gray background and green square icons), while the remaining tabs don’t yet have any content and remain grayed-out. The References Tree (left panel of the Project Tab) contains a folder representing the Project, and nothing else. The 6 context-sensitive buttons in the upper left hand margin of the “tree” panel (‘Add’, ‘Remove from project’, ‘Remove association and remain in project’, ‘Duplicate item’, ‘Select Amplicons associated with item’, and ‘Import data’) start out inactive and grayed-out until some selection is made in the application that can give them context as to what needs to be added or removed (e.g. selecting an object type tab in the right table-view area).

For the example Project, we want to enter a Reference Sequence first, so we click on the right panel’s ‘References’ sub-tab, or References Definition Table. This enables the ‘Add’ button on the left margin (the button turns blue rather than gray) and a blue outline appears around the Definition Table Panel (indicating that the active buttons on the left can operate on the selected item in the Definition Table). Clicking the ‘Add’ button creates a new Reference Sequence entry in the References Definition Table and creates a corresponding reference node in the References Tree (Figure 2‑7).

To define the Reference Sequence, we double-click on the fields in its row, in the References Definition Table. In our example, we edit the default Name “Ref_1” to “EGFR_Exons_18-22”. Note that the tree and table views are linked and editing the Reference Sequence name in the table also changes its name in the tree. Annotations are optional; they are also entered by double-clicking in the corresponding field which, in this case, opens a text entry window (not shown). Finally, we double-click in the ‘Sequence’ field of our Reference Sequence; an ‘Edit Sequence’ window appears in which we paste the “artificial” Reference Sequence covering all five exons, prepared before (Figure 2‑8).