- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2022-06-23 10:59:39+12:00
- Desc:
- Remove a typo
- Permanent Source URI:
- https://models.cellml.org/workspace/874/rawfile/e49ff561204dfdf4692d90837d271bd04fc6286d/Doc/Single-cell response_experiment.rst
Single-cell response experiment
---------------------------------
In the `Single-cell response experiment <Experiments/SMC_KCl_noise.cellml/view>`_, the `isolated cell model <../Components/SMC.cellml>`_ is configured and parameterised with an applied `concentration clamp protocol <../cellLib/Protocols/X_clamp_protocol.cellml>`_.
You can change the parameters of stimulation in the component ``clamp_para``. You can also bypass the parameters in the component ``Para`` and define your own parameters.
The simulation experiment can be obtained by loading the `corresponding SED-ML document <../Experiments/SMC_KCl_noise.sedml>`_ into OpenCOR and executing the simulation. We use the Python script `simFig2 <../Simulation/src/simFig2.py>`_ , `simFig2_1 <../Simulation/src/simFig2_1.py>`_, `simFig2_2 <../Simulation/src/simFig2_2.py>`_, `simFig2_3 <../Simulation/src/simFig2_3.py>`_, `simFig7 <../Simulation/src/simFig7.py>`_ , `simFig7_1 <../Simulation/src/simFig7_1.py>`_, `simFig7_2 <../Simulation/src/simFig7_2.py>`_, `simFig7_3 <../Simulation/src/simFig7_3.py>`_, `simFig7E <../Simulation/src/simFig7E.py>`_ , `simFig7E_1 <../Simulation/src/simFig7E_1.py>`_, `simFig7E_2 <../Simulation/src/simFig7E_2.py>`_, `simFig7E_3 <../Simulation/src/simFig7E_3.py>`_, and `simFig3 <../Simulation/src/simFig3.py>`_ to perform the simulation for the following figures.
The cytosolic calcium concentration of an isolated cell in presence of noise
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Since we do not know the noise strength, we have tried different values to reproduce Fig 2 in the primary paper.
Figure [#]_ shows the cytosolic calcium concentration of an isolated cell in presence of noise with the standard deviation of 0.0015 and 0.002.
.. [#]
.. figure:: ../Simulation/simFig2_1.png
:width: 75%
:align: center
:alt: simFig2_1
Figure [#]_ shows the cytosolic calcium concentration of an isolated cell in presence of noise with the standard deviation of 0.0025 and 0.003.
.. [#]
.. figure:: ../Simulation/simFig2_2.png
:width: 75%
:align: center
:alt: simFig2_2
Dynamics of an isolated SMC stimulated by a receptor-ligand agonist
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Figure [#]_ shows the simulation result of an isolated SMC stimulated by a receptor-ligand agonist (Fig 3 in the primary paper).
.. [#]
.. figure:: ../Simulation/simFig3.png
:width: 75%
:align: center
:alt: simFig3
The cytosolic calcium concentration of an isolated cell by KCl stimulation in presence of noise
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Regarding Fig 7 in the primary paper, we do not know the value of free parameters :math:`E` and :math:`J_{PLC_{agonist}}` apart from the noise strength. We have a few attempts as shown in the following figures.
.. [#]
.. figure:: ../Simulation/simFig7_1.png
:width: 75%
:align: center
:alt: simFig7_1
.. [#]
.. figure:: ../Simulation/simFig7_2.png
:width: 75%
:align: center
:alt: simFig7_2
.. [#]
.. figure:: ../Simulation/simFig7E_1.png
:width: 75%
:align: center
:alt: simFig7E_1
.. [#]
.. figure:: ../Simulation/simFig7E_2.png
:width: 75%
:align: center
:alt: simFig7E_2
