- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-02-18 14:17:34+13:00
- Desc:
- Updating way cellml is written
- Permanent Source URI:
- http://models.cellml.org/workspace/7a8/rawfile/8bb03dd23f61cba2ac9583321a845c02ff6f4155/exposure/exposure_frontpage.rst
About this model
====================
This is a Functional Cell Unit for excitation-contraction coupling in the cardiac cell.
This is a composite module, composed of several individual modules, and merged together in a modular fashion.
**INPUTS:**
- Stimulus current or action potential.
**OUTPUTS:**
- Change in number of myosin binding sites on cross-bridges.
Model status
=============
The current CellML implementation runs in OpenCOR.
Model overview
===================
All components are presented in `bond-graph` form.
Components are made by converting an existing kinetic model and translating into bond-graph form.
.. figure:: exposure/FCU_picture.png
:width: 70%
:align: center
:alt: Components of the model
Components of the model.
A description of the process to find bond-graph parameter is shown in the folder `parameter_finder <parameter_finder>`_, which relies on the:
1. stoichiometry of system
2. kinetic constants for forward/reverse reactions
- If not already, all reactions are made reversible by assigning a small value to the reverse direction.
3. `linear algebra script <https://models.physiomeproject.org/workspace/7a8/file/2488dd73970d607a0d5626a816930732637ec8b4/parameter_finder/find_BG_parameters_composite.py>`_.
Here, this solve process is performed in Python.
Modular description
===================
Components
----------
CellML divides the mathematical model into distinct components, which are able to be re-used in other composite models.
These CellML components are:
- `Sarcoplasmic/endoplasmic Ca2+ ATPase <https://models.physiomeproject.org/workspace/7a5>`_ (SERCA)
- `Phospholamban regulation <https://models.physiomeproject.org/workspace/6d1>`_ (PLB)
- `Ryanodine receptor <https://models.physiomeproject.org/workspace/6e3>`_ (RyR)
- `L-type calcium channel <https://models.physiomeproject.org/workspace/6d7>`_ (LCC)
- `Troponin-C <https://models.physiomeproject.org/workspace/7a9>`_ (TnC)
.. csv-table:: Origin of kinetic model components
:header: "Source", "Components"
:widths: 15, 30
"`Saucerman et al. <https://models.physiomeproject.org/exposure/9766d9bd0325c31e47a31b291e26ccad>`_", "PLB"
"`Luo and Rudy <https://models.physiomeproject.org/e/81>`_", "LCC"
"`Tran et al. <https://models.physiomeproject.org/exposure/815f3cb51960e9c9855e66996c1d1a4c>`_", "SERCA"
"`Stern et al. <https://models.physiomeproject.org/exposure/b060fdbcfae8c7d85e595c24d36ab11b>`_", "RyR"
"`Niederer et al. <https://models.physiomeproject.org/exposure/d3849e5de91b0b94de79c30548a44a79>`_", "TRPN (TnC)"
Each of these blocks is itself a CellML model, complete with bond-graph parameters appropriate for the isolated system.
