Projects

Projects differentiate between various datasets (e.g., different studies) or between different versions of the data (e.g., different methods of assigning OTU names). Projects provide an organizing mechanism for user’s data: the OTU data, associated metadata, and user generated text (notes). Each project is a single data file. The name of the current project is displayed in the upper left corner of the main window. Users may choose to use the data management capabilities of Explicet, which are shown in Figure 2. As shown in the figure, projects may contain one or more workspaces. Workspaces are generally made up of subsets of the data contained in the full project and are wholly contained within the project. Projects and workspaces contain figures, which are tabular and/or graphical representations of data (e.g., a graph of species observed, Sobs, for the data in a project or workspace). Workspaces and figure creation dialogs can be annotated with user generated text describing the how/what/why of the analysis in process, as well as draft figure legend text. All figures created within a project and its workspaces are globally available from the project or any workspace created within that project.

A. New Project

• File → New → Project

• Enter desired project name when prompted

• Click OK to create the new project

B. Copy of Project

• Clones all project-associated data, including OTU tables, filters, and figures.

• File → New → Project from Current Project

• Enter desired project name when prompted

• Click OK to create a copy of the current project

C. Open Existing Project

• File → Open → Project

• Select file

• Click Open to open project

D. Rename Project

• Edit → Project Settings

• Type over existing name in the top line of the pop-up window

• Click Apply to rename current project

E. Save Project

• There are 2 different ways to save a project:

• 1. Click the Save button in upper right corner of any workspace window.

• 2. File → Save / File → Save As

• Note: Quick keys (e.g., Ctrl-s) are not currently supported in Explicet. Explicet does not auto-save, so remember to save often!

F. Close Project

• There are 3 different ways to close out of Explicet:

• 1. Click the Close Project button in upper right corner of any workspace window.

• 2. File → Close → Project

• 3. File → Exit

• Note: If you close a project with multiple workspaces open, the project is saved as-is. The next time you open the project, all workspaces will open exactly as in the previous session.

G. Project Settings

• Project Settings provides a nice layout summarizing all of the project components.

• Edit → Project Settings

  • Edit the Project Name.

  • If the current project is one of several different versions or one of several different studies on the same data, you can record the Project Version number.

  • Record Notes about the project’s specific aims, trends, notes, etc.

  • When Do not import Libraries whose total count is zero is selected, any libraries with no members (e.g., the total number of OTUs in the library is 0) will not be added to the project.

  • Projects may have libraries with no members if Do not import Libraries whose total count is zero is not selected. However, the libraries can be eliminated from computations if you pick the Filter out Libraries whose total count is zero option. In other words, if a library has no members, and Filter out Libraries whose total count is zero is selected, the library will not appear in the workspace window, Alpha Diversity, Beta Diversity, etc.

  • By default, Explicet appends an “_Explicet_Project” extension to filenames in order to help distinguish a project file from other files. This default can be removed by deselecting Append “_Explicet_Project” to Filename.

  • Edit the Column delimiter for Export (character(s) placed between columns); delimiter may be up to 6 characters, enter “tab” for tab.

  • Adjust the # of Decimal Places for Percents in OTU displays.

  • View the date and time the project was created.
  • View the date and time the project was last saved.

  • View the quantity and names of the project’s associated Workspaces, Filters, Figures, Metadata tags, and Libraries.

  • The bottom pane (labeled Project Change Log) tracks all major edits to the project data, including: OTU data imports, metadata imports, deletion of libraries, deletion of OTU lines, renaming of libraries.

• Click Save to keep the changes

  • Click Restore to revert changes made since the last Save. Caution: The Restore function does not apply to Rename Libraries, Remove Libraries or Remove OTU Names. Users cannot undo these actions! For more information on these functions, see Edit Libraries and OTU Names.

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