Pacing protocol syntax¶
In Myokit, pacing is not part of a model but is defined using a separate
pacing syntax. To introduce a pacing current in the model, a variable must be
bound to an external input such as
A common use of this mechanism is to specify a stimulus current
I_stim = amplitude * level where
amplitude is a constant stimulus amplitude (in amperes) and
the dimensionless variable bound to the input
[stimulus] level = 0 bind pace amplitude = 60 [A/F] in [A/F] current = level * amplitude in [A/F]
A pacing protocol definition starts with the segment header
successive line defines a pacing event, I.E. a time when the stimulus is
non-zero. The following five parameters must set (separated by any amount of
The value of the stimulus variable
The time at which this stimulus occurs
The duration of this stimulus
For periodic stimuli, the fourth column specifies the stimulus period. Non-periodic stimuli can be created by entering “0” here.
The number of times a periodic stimulus is given can be specified in the final column, stimuli that are non-periodic or recur indefinetely can use the value “0” here.
Comments may be added by starting lines with
When specifying the time an event starts, the keyword “next” may be used to denote the time at which the previous event ends. This can only be used at the very start of a protocol or directly after a non-periodic event.
A typical example for 0.5ms stimuli occurring every 1000ms (at 1bpm) is:
[[protocol]] #level start length period multiplier 1.0 10 0.5 1000 0
Here, a stimulus of level “1.0” is applied from t=10ms till t=12ms and then again from t=1010ms to t=1012ms continuing indefinitely.
In the following example the stimulus only occurs 3 times:
[[protocol]] #level start length period multiplier 1.0 10 0.5 1000 3
An example for a voltage clamp experiment:
[[protocol]] #level start length period multiplier -80 0 500 0 0 40 500 500 0 0 -80 1000 1000 1000 0
In this example, the pacing level is taken to denote a voltage. At t=0 the voltage is set to -80mV. After 500ms, it changes abrubtly to +40, where it stays for another 500ms. Finally, at t=1000ms it drops down to -80mV again where it stays indefinitely.
This example can be written using the “next” keyword:
[[protocol]] #level start length period multiplier -80 0 500 0 0 40 next 500 0 0 -80 next 1000 1000 0