Location: FCU_ExcitationContraction_Coupling @ 8bb03dd23f61 / exposure / exposure_frontpage.rst

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.