Location: Reproducibility of the computational model of induced pluripotent stem-cell derived cardiomyocytes @ a0bf492b6e68 / Fig10.rst

nima <nafs080@aucklanduni.ac.nz>
2022-02-03 22:14:50+13:00
updated overview.srt
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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 10
Action potential in the baseline model

The developed baseline model including all the channels and current was optimized to reproduce
the spontaneous beating of actional potential as a e key feature of the immature iPSC-CM
phenotype which shows in figure 10.

`Channels.cellml`_ is the main CellML file which shows the I-V curves for different channels fitted to
different experimental data from multiple laboratories.
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 (gating_Ik1, parameter_Ik1, gating_Ikr,
parameter_Ikr, gating_Iks, parameter_Iks, gating_Ito, parameter_Ito, gating_Ica, parameter_Ica, gating_Icat,
gating_Ina, parameter_Ina, gating_If, parameter_If, parameter, unit)
as well as python scripts (`fig10.py`_). In the `fig10.py`_ python script,
required SED-ML file (Channels.sedml) is loaded into the script and by running the code all the required currents
are calculated, and the following figure is reproduced. `fig10.py`_  is used to
generate the simulation and reproduces the graph shown in Figure 11 in the original study.
In order to reproduce Figure 11, once all the files are downloaded to the same folder,
execute the following script from the command line (command prompt):

cd [PathToThisFile]

[PathToOpenCOR]/pythonshell fig10.py

.. figure:: Figure10.png
   :width: 85%
   :align: center
   :alt: time course of the spontaneously beating APs in the baseline model

.. _`Channels.cellml`: https://models.physiomeproject.org/workspace/702/rawfile/a619946dc2f89d6d787cebfbd9b1f2a54f5aa227/Channels.cellml
.. _`fig10.py`: https://models.physiomeproject.org/workspace/702/rawfile/a619946dc2f89d6d787cebfbd9b1f2a54f5aa227/fig10.py