You may have noticed that, so far, there has not been a time component in the simulation that we have done. The simulation required several steps to reach a stable state, but the reason for that was that the network contains several circular parts, so that NetBuilder had to break the cycles (which means that the output of the last symbol in the chain is transferred to the first one only in the next evaluation round). The timer is used to slow the simulation speed down, but its setting bears no relation to the time the processes would, in reality, take to complete.
Time can be introduced, albeit somewhat crudely, by introducing delays between the presentation of a signal to a symbol's input port and its effect on the output. Such delays can be used to simulate 'slow' processes (the user will have to decide which processes are slow, and which ones happen 'instantaneously'). Delays in the transfer of values through links can simulate, for instance, 'slow' transport processes. Delay duration is measured in evaluation cycles ('clock ticks').
Delays can be different for different symbols or links (even if the links originate from the same symbol), but the value for any specific delay is the same in all cells.
Delays can be set by selecting the symbol or link, and pressing the Parameters button on the Symbol parameters toolbar. If you have selected a link, you will be presented with the Link delay values dialog, in which you can specify the delay over the selected link. If you have selected a symbol, the Symbol parameter values dialog will open, in which you can set several parameter values, including the delay parameter, not only for the selected symbol, but for all symbols in the diagram. The significance of the other parameters will be discussed later.
Even though you are allowed to change delays and other parameters when NetBuilder is in Simulation mode, these parameters are fixed during a simulation (in contrast to the symbols' associated values, which change). Strictly speaking, delays are part of the design. Therefore, the shortcuts to the Link delay values and Symbol parameter values dialogs (double clicking the object) are available in the Design mode only.
If you haven's already done so, reset all elements, including the input symbols, as described on the previous page. Set the delay of the gene to 10, and that of the link that connects the gene with the receptor to 15. Make the receptor the Probed Symbol, toggle TF1 to 'on' in cell group A, press Go, and watch what happens.
When you specify a delay value greater than 0, NetBuilder creates an output 'queue' for the symbol or link, which is initially filled with zeros. Whenever a symbol's associated value is updated, the new value is put at the back of the queue, and the value at the front of the queue is taken out, and transferred to the links connected to the output port - if there are any. In the next evaluation round, the contents of the queue all move one place forward again, and so on. The mechanism is the same for delays over links.
The appearance of a symbol (grey or coloured) is determined the value at the back of the queue, i.e. the newly updated value. The colour of a link is determined by the value at the front of the queue, which is about to be transferred from the node to the link.
When you set a symbol's associated value, you change the value at the beginning of the queue. However, input symbols, which have not input of their own, are not updated, and keep their associated value until it is changed by the user. When you change the associated value of an input symbol whose delay is greater than 0, the change will never reach its output links. Therefore, the delay of input symbols must be 0.