fig5.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 05
Transient outward potassium current (Ito) model optimization
The voltage dependent activation and inactivation gating variables were modeled here. experimental iPSC‐CM data collected from Ma et al. (2011), Cordeiro et al. (2013) and Veerman et al. (2016) in order to optimize data specific model. Steady-state inactivation and activation iPSC-CM experimental data, with optimized dataset-specific models for different dataset (Fig. 5 A) Since non of the datasets had both steady-state activation and inactivation data therefore, Inactivation time constant parameters of Veerman et al. (2016) model were optimized with time constant activation from Ma et al. (2011). Cordeiro et al. (2013) model parameters were optimized with steady-state activation parameters from Ma et al. (2011) and steady-state inactivation data from Cordeiro et al. (2013) were used to optimize the model of Ma et al. (2011). All the results are presented in Fig. 5. D. Time constant activation parameters were optimized to ten Tusscher (2004) model which is shown in Fig. 5 C. I-V curves for Ito (Fig. 5. B).
Current_Ito.cellml is the main CellML files which has all the formulation for transient outward potassium current, Its associated Sedml file contains all the simulation settings.
All the CellML files and SED-ML files related to this channel need to be downloaded in a same folder (Current_Ito, gating_Ito, parameter_Ito, parameter, unit) as well as python script (fig5.py). In the python script, required Sedml file (Current_Ito.sedml) is loaded into the script and by running the code following figure is reproduced. fig5.py is used to generate the simulation and reproduces the graph shown in Figure 6 in the original study. In order to reproduce Figure 6, once all the files are downloaded to the same folder, execute the following script from the command line (command prompt):
cd [PathToThisFile]
[PathToOpenCOR]/pythonshell fig5.py
A, optimized activation with dataset-specific model fits. Different colour represent experimental iPSC-CM data from multiple laboratories. B. I-V curves, C, Time constant of Ito activation gate. D, Time constant of Ito inactivation gate.