- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2021-10-11 16:04:27+13:00
- Desc:
- Updated documentation
- Permanent Source URI:
- https://models.cellml.org/workspace/702/rawfile/8deb2452bfa7bfdd5451ba80f0bd3852614361b9/Fig3.rst
About this model
====================
:Original publication: `Colleen E. Clancy, Eleonora Grandi, 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
.. _`Colleen E. Clancy, Eleonora Grandi, et al (2019)`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767694/
**********
Figure 03
**********
Sodium current (:math:`I_Na`) model optimization
*************************************************
For sodium currents, model parameters were optimized to multiple experimental datasets, \
resulting in dataset-specific parameterization instances of the model. \
For each dataset-specific model, external ion concentrations \
and voltage protocols were set to reflect the corresponding experimental conditions. \
All of the experimental data used to optimize the models were collected in iCell iPSC-CMs. \
This process was used to generate dataset-specific models. \
Three separate experimental iPSC-CM datasets are used for sodium current: \
(A) Ma et al. (B) Jalife Immature, (C) Jalife Mature and (D) Baseline model
`act.cellml`_ and `inact.cellml`_ are the main Cellml files which show the probability of \
sodium channel being open and \
close respectively. Their associated Sedml files contain all the simulation settings. \
All the Cellml files and Sedml files need to be download in a same folder \
as well as python script (`fig3-new.py`_). In the python script, required Sedml files are loaded \
into the script and by running the code following figure is reproduced.
.. figure:: Fig3/Figure03.png
:width: 85%
:align: center
:alt: Sodium current (:math:`I_Na`) model optimization
A, steady-state inactivation and activation curves. The sodium current model used in \
the baseline whole-cell model is shown in black. Colours represent distinct experimental \
iPSC-CM data from `Ma et al. (2011)`_ and from immature and mature cell preparations \
from the Jalife lab (`Herron et al. 2016`_). C, INa activation (m-gate) time constants. D, INa fast-inactivation (h-gate) \
time constants. E, INa slow-inactivation (j-gate) time constants. j-gate time constant \
parameters for all INa models were optimized to experimental iPSC-CM data from \
the Kurokawa lab (`Li et al. 2017`_).
.. _`Herron et al. 2016`: https://pubmed.ncbi.nlm.nih.gov/27069088/
.. _`Ma et al. (2011)`: https://pubmed.ncbi.nlm.nih.gov/21890694/
.. _`Li et al. 2017`: https://pubmed.ncbi.nlm.nih.gov/28615142/
.. _`act.cellml`: https://models.physiomeproject.org/e/75e/Channels/act.cellml/view/
.. _`inact.cellml`: https://models.physiomeproject.org/e/75e/Channels/act.cellml/view/
.. _`fig3-new.py`: https://models.physiomeproject.org/e/75e/Fig3/fig3-new.py/view/
