Using Skibsbye in basic bench and cell cable

Question

Hi,

Is there a way I can use Skibsbye as one of the models in the basic bench tutorial? I tried inputting it to the run.py where the models are listed, but I get error " plt.plot(sv_data[:,0], sv_data[:, Vidx[0]+1]) IndexError: list index out of range"

Thanks!

Answer 1

There are two things to consider here:

1) This example only supports a few selected ionic models that were curated to make sure all the features used are existing in these models. As this example is only meant to demonstrate some basic bench functionality not the full set of ionic models is supported. You can manually add other models like the Skibsbye model to line 365 of the run.py file if required.

2) The variable for the transmembrane voltage is called Vm in the Skibsbye model while it is called V in the other models. Thus, plotting only works if you specify the name of the variable to plot: ./run.py --EP Skibsbye --visualize --vis_var Vm