6 Usage

6.1 Main window

Figure 2: Main window of the interface

The main window of the interface is presented in Figure 2.

6.2 Graphical scenario builder

Figure 3: Graphical scenario builder

The window of the Graphical scenario builder is presented in Figure 3.

6.3 Constructing a new workspace

Figure 4: The WM file.

1. middle click in builder window places the file WM (Figure 4).
2. shift+middle click in builder window places the from_file WM. right click on the WM opens the pop-up menu. Options opens the File Selection dialog. The from_file WM lets the user to process data stored on local machine.
3. Other pop-up menu items:

   Copy – Copy node to clipboard,

   Paste – Paste the previously copied node at the location of mouse pointer,

   Delete – Delete node,

   Help – Open the short description of the selected WM,

   View output – If a node was executed and the mouse pointer is placed on the node output port this item will display the port output.

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   Figure 5: Set the parameters, timeout and label of new node  strel.

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4. Select a WM from the list displayed in the main window by left click on its name. The middle click in the builder window window will place the WM at the location of mouse pointer. Use Options item of the pop-up menu to set the parameters, timeout and label of new node. The double click opens the same dialog, e.g. for WM srel 5.
5. Use left click to select the display node from the list shown in the main window. The middle click in the builder window will place this node at the location of mouse pointer. Use Options item of the pop-up menu to set the parameters, timeout and label of new node.

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   Figure 6: Making connection. Step 1.

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   Figure 7: Making connection. Step 1. Result.

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   Figure 8: Making connection. Step 2.

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   Figure 9: Making connection. Step 2. Result

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6. To connect nodes left click on the output port of the first node – Figure 6. The port and all outgoing connections will be colored red – Figure 7. left click on the input port of the target node – Figure 8. Connection will appear – Figure 9.
7. The processing results can be saved on the local machine. To do so ctrl+middle click in the builder window window. This places the to_file node. Go to the Options menu item and specify the output file in the File Save dialog window.
8. To delete an existing connection repeat the operations listed in 9.
9. The addition/deletion of node or connection can be undone and redone by using the Undo and Redo buttons of the builder window toolbar (1).
10. Other buttons of the builder window toolbar:

    Save As – open the File Save dialog window to specify the location and name of the file to which workflow will be saved,

    Save – save workflow,

    Close – close application,

    Run – run workflow,

    Stop – stop the execution of workflow,

    Rew – rewind workflow to the start,

    Compile – compile workflow to WM.

6.4 Work with existing workspace

Figure 10: Running workflow.

1. The execution is started by pressing the Run button of the builder window toolbar, see Figure 10, where the status of the node is displayed with a color.
2. The execution stops, if the Stop button is pressed. The run will continue from the break point if the Run button is pressed again. The Rew button (rewind) clears all intermediate results.
3. If the options of a node were changed by using the Options dialog then the execution of workflow stops and all downstream nodes are cleared starting from this node. If the options of a node were changed by using the Options dialog box then the execution of workflow stops and all nodes located downstream from the modified node are cleared.
4. If a connection is removed or changed then the execution of workflow stops and all downstream nodes are cleared starting from this connection.
5. The temporary storage is freed on exit and rewind.

6.5 Compiling the workflow

Figure 11: Compiling workspace.

The compilation is illustrated in Figure 11. Compilation results in four files placed in a new directory specified in the File selection dialog opened by pressing the Compile button. The name of the directory is the same as the name of the new WM.

The following files are generated:

• <name>.pl – the Perl script that serves as the WM executable and runs workflow in the komet interpreter,
• <name>.in – the input Ports of new WM,
• <name>.out – the output Ports of new WM,
• <name>.ui2 – the user interface displayed under the Options menu in bambu.

6.6 Several workspaces or several datatsets

Figure 12: Run workspace in the background.

To merge two workspaces use the following commands:

To run workspace in the background open the workspace and look through all to_file and from_file nodes. They should contain not the real filenames but only the "suffixes" to identify correct inputs and produce correct outputs based on the embryoname. The paths will be corrected at runtime only suffixes matter. Go to Workspace/Apply menu 12. Select workspace, the folder that contains input images, the output folder, the server can be left unchanged (localhost:7778) and type your email. If the check box is checked the workspaces for each embryo in the output folder with correct paths. When you click OK the separate process is started that does the job so you can close the main window. It writes logs and states to the output folder.

Another option is to generate workspaces for all embryos and then process them. To generate them to the following: