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2. Example Amplicon Project Design and Analysis : 2.2 Project Setup in the AVA Software : 2.2.2 Creating a New Project
2.2.2
Creating a New Project
Since we want to create a new Project, we click the “New” button. (The “Open” button can be used to load a pre-existing Project.) The “New Amplicon Project” window opens, where we can specify the ‘Name’, ‘Location’, and ‘Description’ for the new Project (Figure 2‑3). Note that since the ‘Generate location based on name’ box is checked, the ‘Name’ and ‘Location’ fields are linked such that as we type a name to replace the ‘DefaultName’ in the ‘Name’ field, the ‘DefaultName’ portion of the ‘Location’ will dynamically update to match the content of the ‘Name’ box; this is an easy way to ensure that the same name is used for the Project and for the folder that contains it (the “Location”), which is usually what one would want to do.
Figure 2‑3: The New Amplicon Project window
To keep things simple, we initially leave the ‘Name’ field alone and first select the ‘Location’ we want. The folder icon to the right of the ‘Location’ field opens the “New Project Parent Location” window which allows us to navigate the file-system easily (Figure 2‑4). The object is to identify a parent location where we want to store Project directories (as opposed to the full path to this particular new Project directory), providing a standard base of operations. It is important to choose a directory where we have both read and write permissions.
Figure 2‑4: The New Project Parent Location window
To pursue our example, let’s assume that we have read and write permissions in the ‘/data/ampProjects’ directory on our local system, and that we chose ‘ampProjects’ as the parent location directory (Figure 2‑4). The path to this directory is used to form a ‘File Name’. Clicking ‘OK’ returns us to the “New Amplicon Project” window, where the path we just chose is reflected in the ‘Location’ field: ‘/data/ampProjects/DefaultName’. Editing the contents of the ‘Name’ field to ‘myFirstTestProject’ (with the ‘Generate location based on name’ box checked), provides a full path for the Location of the new Project (Figure 2‑5). This Figure also shows a short annotation entered in the ‘Description’ field.
Figure 2‑5: The New Amplicon Project window, with the Name, Location and Description of the new project
Clicking ‘OK’ at this point closes the “New Amplicon Project” window, creates the Project and the Location (including a proper subdirectory structure for the functioning of the Project computation and result storage), and opens the new Project in the AVA main window, in its “Project” tab (see next section).
 
Although this Project does not use MIDs, the 454Standard MID set is automatically loaded when a new Project is created (see section 4.4), which is why 14 MIDs will be present in the newly created project.