- 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/Fig5.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/
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Figure 05
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Transient outward potassium current (:math:`I_to`) 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 :math:`I_to` (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
.. figure:: Experiments/Figure05.png
:width: 85%
:align: center
:alt: Transient outward potassium current model optimization
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 :math:`I_to` activation gate. D,
Time constant of :math:`I_to` inactivation gate.
.. _`ten Tusscher (2004)`: https://journals.physiology.org/doi/full/10.1152/ajpheart.00794.2003/
.. _`Ma et al. (2011)`: https://pubmed.ncbi.nlm.nih.gov/21890694/
.. _`Veerman et al. (2016)`: https://www.nature.com/articles/srep30967/
.. _`Cordeiro et al. (2013)`: https://pubmed.ncbi.nlm.nih.gov/23542310/
.. _`Current_Ito.cellml`: https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/Current_Ito.cellml
.. _`fig5.py`: https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Experiments/fig5.py
