The library of currently available modules contains several more symbols. Their functions are described below.
In some simulations, it may be necessary to carry out a comparison of the size of two signals. NetBuilder provides five functions that carry out such comparisons: ‹ (less than), › (greater than), ≤ (less than or equal to), ≥ (greater than or equal to), and = (equal to). They are found under Functions: Operation, and their output is 1.0 if the result of the comparison is true, and 0.0 if it is false. The main input (a) is taken to be the first argument, the secondary input (b) is the second argument: a < b, a > b, a ≤ b, a ≥ b, a = b; as in the example below.
In addition to the simple components that have a single input port, NetBuilder provides components with a second input port (Component: Interaction: 'And' activation or 'Or' activation). These components need the input of one or more other symbols that are connected to their second input port to become active. They calculate their output as follows:
yand-activation = x1 × { (x2 / (x2 + 1)) × (x3 / (x3 + 1)) }
yor-activation = x1 × { (x2 / (x2 + 1)) + (x3 / (x3 + 1) × (1 - (x2 / (x2 + 1))) }
These equations describe non-cooperative binding of the input components 2 and 3 (of concentrations x2 and x3, relative to the equilibrium dissociation constants of the complexes). In the case of 'And'-activation, x1 and both x2 and x3 need to be greater than zero to produce an output greater than zero, in the case of an 'Or'-activation it is sufficient if x1 and either x2 or x3 are greater than 0.0.
Negated input (inhibition) is interpreted as 1 - x/(x + 1), as in the example below:
Here:
yor-activation = x1 × { (1 - (x2 / (x2 + 1))) + (x3 / (x3 + 1) × (1 - (1 - (x2 / (x2 + 1)))) }
A 'switch' is a component that is switched on by an activator input, and then stays on for the duration of the simulation. Only when the switch is on, the main input is multiplied by the scaling factor, and transferred to the output port. The switch from off to on takes place when the activator input is at least 1.0. Switching is irreversible, and the only way to turn a switch off is by manually resetting it, using the Reset dialog.
