- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2022-02-03 11:12:12+13:00
- Desc:
- Ca_analysis.py added to figure 9 script so we do not need 2 python scripts for one figure.
- Permanent Source URI:
- https://models.cellml.org/workspace/702/rawfile/3d6d9b2f873781d62bb1c85317a334b46e341c53/Fig6.rst
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
.. _`Kernik et al. (2019)`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767694/
************
Figure 06
************
Slow delayed rectifier potassium current (:math:`I_Ks`) model optimization
****************************************************************************
The voltage dependent activation gating variables were modeled here.
experimental iPSC‐CM data collected from `Ma et al. (2011)`_ and two other independent datasets
from `Ma et al. (2015)`_ 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. 6 A)
Parameters in all models were parameterized using the activation time constants from `Ma et al. (2011)`_ (Fig. 6. B). and I-V curves for
:math:`I_Ks` (Fig. 6. C).
`Current_Iks.cellml`_ is the main CellML files which has all the formulation for slow delayed rectifier 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_Iks, gating_Iks, parameter_Iks, parameter, unit)
as well as python script (`fig6.py`_). In the python script, required Sedml file (Current_Iks.sedml) is loaded
into the script and by running the code following figure is reproduced. `fig6.py`_ is used to
generate the simulation and reproduces the graph shown in Figure 7 in the original study.
In order to reproduce Figure 7, once all the files are downloaded to the same folder,
execute the following script from the command line (command prompt):
cd [PathToThisFile]
[PathToOpenCOR]/pythonshell fig6.py
.. figure:: Experiments/Figure06.png
:width: 85%
:align: center
:alt: Slow delayed rectifier potassium 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 :math:`I_Ks` activation gate. C, I-V curves.
.. _`Ma et al. (2011)`: https://pubmed.ncbi.nlm.nih.gov/21890694/
.. _`Ma et al. (2015)`: https://pubmed.ncbi.nlm.nih.gov/25889101/
.. _`Current_Iks.cellml`: https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/Current_Iks.cellml
.. _`fig6.py`: https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Experiments/fig6.py
