How to implement a bolus injection

Sometimes a certain amount of a chemical compound is added during the simulation of an experiment. This mean that the state variable of the respective compound changes it's value by a certain amount at a certain point of time.

Such event can be modeled by an additional input function:

INPUTS
BolusInjection   C  nM  conc.  "bolus_amount * (1/sqrt(2*pi*injection_duration^2)) * exp(-(t - injection_timepoint)^2/(2*injection_duration^2))"

The function is a scaled normal distribution (given that t indicates the independent variable) with area under the curve given by the value of bolus_amount. The injection time point is given by injection_timepoint and the duration by injection_duration.

Additionally, one has to specify a reaction that adds this input function to the respective state variable (here ProteinA):

REACTIONS
              ->  ProteinA        CUSTOM "BolusInjection"

In the folder /Examples we provide some showcase applications Bolus_Injection_Test that can be used as a starting point for a new modeling project.

In this example a bolus of 5 nM is injected at time point 40 minutes over a period of 1 minute, as the counter state ProteinC indicates.