fig8-new.py

About this model

Original publication:
 Kernik et al. (2019): "A computational model of induced pluripotent stem-cell derived cardiomyocytes incorporating experimental variability from multiple data sources" J Physiol. 2019 Sep 1; 597(17): 4533-4564.
DOI:https://dx.doi.org/10.1113%2FJP277724

Figure 08

Pacemaker/funny current (If) model optimization

The voltage dependent activation gating variables were modeled here. experimental iPSC‐CM data collected from Ma et al. (2011) and Kurokawa Lab Li et al. (2017) in order to optimize data specific model. Activation gate parameters were optimized using the steady-state activation and activation time constants from experimental data (Fig. 8. A and B).

act_inact.cellml is the main CellML file which shows the probability of transient outward potassium channel being open orclose. Its associated SED-ML file contains all the simulation settings. All the CellML files and SED-ML files need to be download in a same folder (act_inact, gating, parameter, unit) as well as python script (fig8-new.py). In the python script, required SED-ML file is loaded into the script and by running the code following figure is reproduced. fig8-new.py is used to generate the simulation and reproduces the graph shown in Figure 8 in the original study. In order to reproduce Figure 8, once all the files are downloaded to the same folder, execute the following script from the command line (command prompt):

cd [PathToThisFile]

[PathToOpenCOR]/pythonshell fig8-new.py

Pacemaker/funny current model optimization

A, optimized steady-state activation with dataset-specific model fits. Different colour represent experimental iPSC-CM data from multiple laboratories. B, Time constant of If activation gate.