To obtain a 'view of the nucleus' in one particular cell, go from the Design mode into the Simulation mode by pressing the Simulate button, the only button on the Simulation toolbar that is enabled at this stage. If everything is alright, all previously enabled buttons on the Design toolbar will be disabled, but the top button (Edit) will enable you to go back to the Design mode. The Simulate button will be disabled, but all most buttons on the Simulation toolbar can be used now.
Upon the switch from Design into Simulation mode, NetBuilder performs a so-called 'topological sort' of the network. This involves making a list of 'input symbols', which are the ones that have no input themselves - in the example network TF1 and TF2 are input symbols. Then, the symbols that 'depend on' the input symbols (here: the gene; follow the arrows) are put next in the list, and so on, until all symbols are listed. Sometimes the dependences are circular (like a snake biting itself in the tail), in which case NetBuilder line arises the circle by designating one of the members of the circle as the last one in the list. The process is somewhat complicated by the presence of multiple connected cells - the multicellular network is a network of identical intracellular networks.
The example contains several circles. 'General' genes always introduce circles (for instance there is a circle from the gene via the 'And' function, via the 'Or' functions, back to the gene again). Furthermore, the cells are also connected in a circle (A g B1 g B2 g A).
NetBuilder will not allow you to go into the Simulation mode when you have forgotten to specify a cell, or when there are loose connections somewhere in the network.
The View of the Nucleus will look something like this:
The symbols are all grey, because they are all 'inactive'.
As stated above, the View of the Nucleus visualises the state of the network in the nucleus of one particular cell, or cell group (cells that have been grouped in the Design mode function to all aims and purposes the same as a single cell, and in the following the term 'cell' can signify a single cell, as well as multiple grouped cells). The cell whose state is currently displayed is called the Open Cell, and is indicated by a thick black line around its contours. Thus, in the picture above, cell group A is the Open Cell. To change to another cell, select the cell that you want to 'open' by single left clicking it, and press the Probe button, the topmost enabled button on the Simulation toolbar. There is always one, and just one open cell: opening another cell will close the one that was previously open.
You will have noticed that the 'contents' of the cells are also grey, and not red as in the Design mode. However, cells contain whole networks, and cannot be 'active' or 'inactive' like other symbols. What, then is the function of the cell colour? To understand this, select TF1 (by a single left click) and hit the Probe button again. A red rectangle will appear around its boundary, to indicate that TF1 is now the Probed Symbol. (Note: if the red rectangle does not appear, you may have inadvertently selected TF1's name label. The best thing to do is to move the name label temporarily out of the way, and try to select TF1 itself. Keep an eye on the document status bar, which will say either "Label", when you are about to select the name label, or "TF1", when you are hovering above TF1 itself.)
Now, with TF1 still selected (if it isn't, select it again) press the Toggle button on the Simulation toolbar. The Toggle command is used to toggle the state of input symbols in the Open Cell between 'on', 'active', and 'off', 'inactive'. As TF1 is now active, its colour will have changed from grey to red, and its line thickness will have increased slightly. Furthermore, cell group A is now coloured red as well:
Now, have a look in one of the other cells, e.g. cell B3 (select cell B3 and hit Probe). In B3, TF1 is grey, because you have switched it on in cell group A only, because that was the open at the time you hit the Toggle button. However, cell group A is still red, to indicate that the Probed Symbol is active in those particular cells.
It is not necessary to have a Probed Symbol, and you can remove the red boundary (and the Probed Symbol status) by selecting the Probed Symbol and pressing the Probe button. It is not possible to have more than one Probed Symbol: designating the Probed Symbol status to a particular symbol will remove that status from the current Probed Symbol.
Making a symbol the Probed Symbol can be compared with putting a fluorescent label onto a particular cellular component. If the tag (and thus the tagged component) is present in a cell, the cell will fluoresce, if not, it will appear dull.