Before you start:We do hope that it won't happen too often, but NetBuilder does sometimes crash without giving you the opportunity to save your work. Therefore, we recommend that you save your diagrams regularly while you are working on them. If NetBuilder crashes, it would be highly appreciated if you could report the conditions under which the crash occurred to the developers, who will then try to rectify the error in the program.
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The regulatory apparatus is hardwired in the genomic DNA, and is the same in each cell that belongs to a particular organism. NetBuilder allows you to set up an organism consisting of one or more cells, create the GRN, and specify intercellular interactions. NetBuilder requires the specification of at least one cell.
Click the Cell button on the Design toolbar, and move the cursor over the canvas to the position where you want to place the cell. Notice that the cursor has changed from a simple arrow (the Ready cursor) to the Insert Symbol cursor. Drop the cell by left clicking once. The cursor changes back to the Ready arrow, to indicate that NetBuilder is ready to receive new commands.
Click the Cell button again, and move the cursor onto the canvas. Now click the right mouse button once, and notice that the cursor changes from the Insert Symbol cursor back to the Select arrow, and that no new cell has been put on the canvas. This is how you prevent a command that you have just given from being carried out.
After an editing command has been carried out, you can (usually) undo it by selecting Edit:Undo from the menu.
Move the cursor over one of the symbols, and notice that it changes its shape to the Drag cursor, two perpendicular double-headed arrows. You can now select the symbol underneath the cursor by left clicking. If you keep the left mouse button pressed, you can drag the symbol to some other place on the canvas. Move the cursor over the selected symbol, and notice its eight “handles”, indicated by small squares, that can be used for resizing the symbol. To resize, move the cursor on top of one of the handles, and notice that it changes into a single double-headed arrow (the Resize cursor). Hold the left mouse button down, move the mouse, and observe what happens. Other symbols can be selected or unselected by left clicking them. To select more than one symbol, hold down the Ctrl or the Shift key whilst clicking the symbols you want to select. You can also select multiple symbols by putting the cursor in the corner of an imaginary square around the symbols you wish to select, and dragging the mouse to the opposite corner whilst holding the left button down. Experiment with moving and resizing, and create an “organism” that looks like the one below.
Zoom into the picture by pressing the zoom button (the cursor changes into a magnifying glass), move the cursor to the top right of the area that you want to zoom into, hold the left mouse button down, and drag the cursor to the bottom left corner of the zoom area. Press the Select button to go back to the Ready cursor. To restore the 'normal' view (100%), press the Zoom normal button. To fit all symbols into the open window, press Zoom to fit, and to zoom into a specific symbol, press Zoom to selection.
Select the top two cells, and click the right mouse button. Right clicking a symbol or multiple selected symbols will bring up a popup menu that can be used, among other things, to group cells, and to change a symbol’s properties. Select the Grouping:Group command. The two cells are now grouped, and respond as if they were a single cell. At present, cells are the only symbols that can be grouped. The distinction between single cells and cell groups is purely aesthetic, and there is (at present) no functional difference between the two. If the properties of cells are different, they must be modeled with separate symbols.
Right click the single cell, and select Properties… from the popup menu. A new tabbed dialog box opens. You can change the cell’s name by clicking the General tab (in case the General sheet is not on top) and changing the text in the box labeled “Name “. Rename the top group “A”, and the three cells underneath “B1”, “B2”, and “B3” (without the quotes).
Other symbol properties, such as line and fill colour and style, can also be changed via the Properties dialog.
In addition to the method outlined above, you can also rename a symbol by holding down the Ctrl key, and double clicking the symbol. A label containing the name of the symbol appears (and disappears when you double click again with the Ctrl key down). If you now double click the label itself, the label text is selected, and you can change it. This will change the name of the symbol.
Labels are text boxes that can be selected, changed, and moved individually. However, they belong to a particular symbol, and when the symbol itself is moved the label will retain its position with respect to its parent symbol - it moves with the symbol.
When you select a cell, the Name and Caption buttons on the Symbol Parameters toolbar become active, as in the picture below, in which cell B3 is selected. The Name button is in the 'on' position, which signifies that the currently selected symbol has a name label. It will go 'off' when it is clicked, and at the same time the name label will disappear. The Caption button (with the button text 'label') is in the off position. When it is pressed, a new label, with initial text 'Caption' appears. This label is unrelated to the name of the symbol, and can be used for annotations. The third button, Type, which is disabled when a cell is selected, toggles another label indicating the function type (see further). Visualise the name labels of each cell.
Symbols can be copied, or cut out and pasted onto another position on the canvas, by selecting it, and issuing the Copy, Cut, or Paste commands from the Edit menu, Main toolbar, or the menu that pops up on right clicking a symbol. Copied or cut symbols are put on the clipboard, and can also be pasted into other programs (e.g. MS Office) that use the clipboard.
It may be difficult or even impossible to select a particular component. This happens when there is an object in the foreground that is bigger than the one you are trying to select. If this happens, select the bigger object, and choose Edit:Structure:Send to back from the menu. You will now be able to select components that were previously ‘behind’ the bigger object.