Main Screen Overview

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Figure 3.1: The opening window has various navigation options, including links to recent projects and shortcuts to open new projects.

3.1.1 The Menu Bar

The opening screen’s menu bar has three drop-down menus:

  • The File Menu which lets you open a new, old or recent project or quit.
  • The Tools Menu which lets you set options for updates and new projects, run scripts, start up a Python shell and update HelixTree.
  • The CNAM menu which allows you to do copy number analysis if that module is licensed.
  • The PBAT menu which allows you to do family-based analysis if the PBAT module is licensed.
  • The Help Menu, as well as the F1 key or Help icon, brings up a Help window with information regarding the window you have open.

3.1.2 New Project

HelixTree first requires the creation of a project to which data files will be imported. Creating a project adds a Project Node to the Project Navigator window (the left window pane). Once you have created a project file, you are able to import a legacy (.ghd) data set or convert a source data set from its native format to a platform-independent HelixTree internal binary format (.ghp). (To open a previously saved project skip to Section 3.4.1 Open Project.)

ASCII space-separated and comma-separated file formats are supported directly by HelixTree. A third party package, Stat/TransferTM, is integrated into HelixTree to import from additional data formats such as SASR○, Microsoft ExcelR○, and various databases such as OracleR○, SQL ServerR○, AccessR○, Sybase○R and DB2R○. Importing a data set creates two new Navigator Nodes under the Project Node: one for the data set and another for the Spreadsheet Viewer. The Spreadsheet Viewer automatically opens as part of the import process.

From the opening screen, click on the File->New Project menu options or click on the first icon on the left on the tool bar. The New Project window appears (Fig. 3.2) prompting you to specify a name for the new project. Enter a name for your new project. Under the Project Name prompt is another entry showing the intended file folder where the project will be located. The Project Name is also the default name of the new folder that will hold all of the project data. Every project has its own folder.

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Figure 3.2: The New Project dialog window for entering the name of the new project

To change the Project Location (the parent folder that will contain the new project folder), click on the Browse button and designate the new location in the Browse For Folder dialog window (Fig. 3.3). Press OK when done to return to the New Project dialog. Fig. 3.3 shows the HelixTree installation folder selected as the parent folder for the new project.

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Figure 3.3: The Browse For Folder window for selecting a parent folder for the project

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Figure 3.4: The New Project dialog with the new project named.

Notice that the project name is automatically appended to the project location that was previously specified. It now becomes a new folder on your system. To complete the project creation process, click the Create Project button.

There is now a new sub-folder of HelixTree called Discovery with a new project file, Discovery.ghp, in the Discovery folder. The Discovery.ghp file will hold important information about your project and it is the file to select when you want to re-open this project at a later date.

The new project has now been created and is displayed in HelixTree’s Project Navigator Window with the word Project appended as shown in Fig. 3.5.

To skip to an overview of data import go to section 4 .

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