The strength of biological signals is, of course, not just 0 or 1, or even low or high, it is zero or larger. Therefore, NetBuilder allows any values equal to or greater than 0.0 to be exchanged between nodes.
In a continuously valued simulation, logical operations like 'And', 'Or' and 'Not' can still be used, but data may also be added up, multiplied, or raised to a particular power.
It is important to realise that data transferred from one node to the next in a NetBuilder network are dimensionless. Values are determined by the sender, but only 'mean' something to the receiving nodes. Therefore, it is necessary to know how each type of symbol interprets its input. Below, we shall explain how the most important symbols ("Modules") interpret their input and produce their output, using the network you have created in this tutorial as an example where necessary.
In addition to the delay parameter, there are several other parameters that need to be defined for each symbol before starting a simulation of a continuously valued network. The Symbol parameter values dialog is opened as described previously (pressing the Parameter values button on the Symbol parameters toolbar, or double clicking a symbol when NetBuilder is in the Design mode).
After performing the transformation specific for each type of module, the result is raised to the power of P, and multiplied by a scaling factor F before the result is transferred to the output port. Thus, P and F need to be set, but are fixed at 1.0 for some types of symbols and cannot be edited.
It is also possible to change the threshold for the transition from grey to coloured using the Symbol parameter values dialog.
To start a continuously valued simulation, select the menu option Simulation : Simulation type : Continuous (which is the default type). Set the colour thresholds of both logical functions, the receptor, and the gene to 0.5, and set the scaling factor and the power ("Hill coefficient") of TF3 to 10 and 4, respectively.
Reset all symbols to 0.0, toggle TF1 to 1.0, press Go, and observe what happens.
On the next pages we describe how the various symbols interpret their input, and transform the data to produce output.