- 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/Components.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/
************
CellML files
************
CellML can build a model in a modular way which divides the model
into distinct modules, which can be re-used.
The main CellML files:
- `Components <Components>`_ which include:
- Main file that put all the other required files together: `Channels <https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/Channels.cellml>`_
this file is the main CellML file which is the top model in the hierarchical modular
presentation and rest of the files need to be imported here in order to run the simulation.
- These files have the formulation for calculating each channel's current (for instance: *Current_Ik1*): `Current_Ik1 <https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/Current_Ik1.cellml>`_
- Probability of channels gates being open or close: (for instance: *gating_Ik1*): `gating_Ik1 <https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/gating_Ik1.cellml>`_
these files has the fomulation for calculating the probability of channels gates being
open or close and also the activation/inactivation time constants.
gating files need to be imported into their associated current files in order to run the simulation and calculate the Voltage-dependent activation/inactivation gating variables (:math:`X_act` and :math:`X_inact`).
- General file for required parameters: `parameter <https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/parameter.cellml>`_
This file is a general file, specific parameters for calculating the probability of each channel's gate being
open or close are presented in associated python script.
- some of the channels have their own parameters which are collected in specific file (for instance: *parameter_Ik1*): `parameter_Ik1 <https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/parameter_Ik1.cellml>`_
- All the required units for this simulation: `unit <https://models.physiomeproject.org/workspace/702/rawfile/e388d6821ddf07b4f8ffb23597eff4ffe31a8efb/Components/unit.cellml>`_
