- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2021-07-06 11:22:35+12:00
- Desc:
- Change the figures size to fit the Physiome paper;
Adjust the solver setting to remove the notch in Fig6.
Minor editting in README.
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/692/rawfile/b98a10f69ee76a70243efdb648c598db5a866a2c/Experiments/Patch_clamp_experiment.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Patch_clamp_experiment" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="../Components/units.cellml">
<units name="ms" units_ref="ms"/>
<units name="pA" units_ref="pA"/>
<units name="mV" units_ref="mV"/>
</import>
<import xlink:href="../Components/Clamped_current.cellml">
<component component_ref="Clamped_current" name="Clamped_current"/>
</import>
<import xlink:href="Patch_clamp_protocol.cellml">
<component component_ref="Patch_clamp_protocol" name="Patch_clamp_protocol"/>
</import>
<import xlink:href="../Components/time.cellml">
<component component_ref="time" name="time"/>
</import>
<import xlink:href="../Components/default_values.cellml">
<component component_ref="model_parameters" name="model_parameters"/>
<component component_ref="initial_conditions" name="initial_conditions"/>
</import>
<!-- Connect the time source variable to the model and stimulus protocol -->
<connection>
<map_components component_1="time" component_2="Patch_clamp_protocol"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="time" component_2="Clamped_current"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- Connect the parameters to the protocol definition -->
<component name="Clamp_parameters">
<variable initial_value="1000" name="t_ss" public_interface="out" units="ms"/>
<variable initial_value="-100" name="V_actHolding" public_interface="out" units="mV"/>
<variable initial_value="-90" name="V_actTest" public_interface="out" units="mV"/>
</component>
<connection>
<map_components component_1="Clamp_parameters" component_2="Patch_clamp_protocol"/>
<map_variables variable_1="t_ss" variable_2="t_ss"/>
<map_variables variable_1="V_actHolding" variable_2="V_actHolding"/>
<map_variables variable_1="V_actTest" variable_2="V_actTest"/>
</connection>
<!-- and connect the actual stimulus current to the model -->
<connection>
<map_components component_1="Patch_clamp_protocol" component_2="Clamped_current"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<!-- SED-ML (and CSim simulation description above) is only able to address variables at the top level of the model hierarchy, so we need to define the variables we want SED-ML to be able to address here. -->
<component name="outputs">
<variable name="time" public_interface="in" units="ms"/>
<variable name="V" public_interface="in" units="mV"/>
<variable name="I_ion" public_interface="in" units="pA"/>
<variable name="I_CaL" public_interface="in" units="pA"/>
<variable name="I_CaT" public_interface="in" units="pA"/>
<variable name="I_Kv" public_interface="in" units="pA"/>
<variable name="I_BK" public_interface="in" units="pA"/>
<variable name="I_Na" public_interface="in" units="pA"/>
<variable name="I_NCX" public_interface="in" units="pA"/>
<variable name="I_NaK" public_interface="in" units="pA"/>
<variable name="I_NsNa" public_interface="in" units="pA"/>
<variable name="I_NsK" public_interface="in" units="pA"/>
<variable name="P_CaL" public_interface="in" units="dimensionless"/>
<variable name="P_CaT" public_interface="in" units="dimensionless"/>
<variable name="P_BK" public_interface="in" units="dimensionless"/>
<variable name="P_Kv" public_interface="in" units="dimensionless"/>
<variable name="P_Na" public_interface="in" units="dimensionless"/>
<variable name="d_CaT" public_interface="in" units="dimensionless"/>
<variable name="f_CaT" public_interface="in" units="dimensionless"/>
<variable name="x_Kv" public_interface="in" units="dimensionless"/>
<variable name="y_Kv" public_interface="in" units="dimensionless"/>
</component>
<!-- and connect the output variable definitions to their actual source in the model -->
<connection>
<map_components component_1="Clamped_current" component_2="outputs"/>
<map_variables variable_1="I_ion" variable_2="I_ion"/>
<map_variables variable_1="I_CaL" variable_2="I_CaL"/>
<map_variables variable_1="I_CaT" variable_2="I_CaT"/>
<map_variables variable_1="I_Kv" variable_2="I_Kv"/>
<map_variables variable_1="I_BK" variable_2="I_BK"/>
<map_variables variable_1="I_Na" variable_2="I_Na"/>
<map_variables variable_1="I_NCX" variable_2="I_NCX"/>
<map_variables variable_1="I_NaK" variable_2="I_NaK"/>
<map_variables variable_1="I_NsNa" variable_2="I_NsNa"/>
<map_variables variable_1="I_NsK" variable_2="I_NsK"/>
<map_variables variable_1="P_CaL" variable_2="P_CaL"/>
<map_variables variable_1="P_CaT" variable_2="P_CaT"/>
<map_variables variable_1="P_BK" variable_2="P_BK"/>
<map_variables variable_1="P_Kv" variable_2="P_Kv"/>
<map_variables variable_1="P_Na" variable_2="P_Na"/>
<map_variables variable_1="d_CaT" variable_2="d_CaT"/>
<map_variables variable_1="f_CaT" variable_2="f_CaT"/>
<map_variables variable_1="x_Kv" variable_2="x_Kv"/>
<map_variables variable_1="y_Kv" variable_2="y_Kv"/>
</connection>
<connection>
<map_components component_1="outputs" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<!-- and connect the time output to the source time variable -->
<connection>
<map_components component_1="Patch_clamp_protocol" component_2="outputs"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<!-- We connect the default parameters through to the model-->
<connection>
<map_components component_1="model_parameters" component_2="Clamped_current"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="V_cell" variable_2="V_cell"/>
<map_variables variable_1="Cao" variable_2="Cao"/>
<map_variables variable_1="Ko" variable_2="Ko"/>
<map_variables variable_1="Nao" variable_2="Nao"/>
<map_variables variable_1="Q10Ca" variable_2="Q10Ca"/>
<map_variables variable_1="Q10K" variable_2="Q10K"/>
<map_variables variable_1="Q10Na" variable_2="Q10Na"/>
<map_variables variable_1="T0CaL" variable_2="T0CaL"/>
<map_variables variable_1="T0CaT" variable_2="T0CaT"/>
<map_variables variable_1="T0K" variable_2="T0K"/>
<map_variables variable_1="T0Na" variable_2="T0Na"/>
<map_variables variable_1="n_CRT" variable_2="n_CRT"/>
<map_variables variable_1="n_CaM" variable_2="n_CaM"/>
<map_variables variable_1="CRT_total" variable_2="CRT_total"/>
<map_variables variable_1="CaM_total" variable_2="CaM_total"/>
<map_variables variable_1="K_D_CRT" variable_2="K_D_CRT"/>
<map_variables variable_1="K_D_CaM" variable_2="K_D_CaM"/>
<map_variables variable_1="g_CaL" variable_2="g_CaL"/>
<map_variables variable_1="g_CaT" variable_2="g_CaT"/>
<map_variables variable_1="g_Kv" variable_2="g_Kv"/>
<map_variables variable_1="g_BK" variable_2="g_BK"/>
<map_variables variable_1="g_Na" variable_2="g_Na"/>
<map_variables variable_1="g_NsNa" variable_2="g_NsNa"/>
<map_variables variable_1="g_NsK" variable_2="g_NsK"/>
<map_variables variable_1="tau_dCaT" variable_2="tau_dCaT"/>
<map_variables variable_1="tau_xKv" variable_2="tau_xKv"/>
<map_variables variable_1="tau_yKv" variable_2="tau_yKv"/>
<map_variables variable_1="k_on" variable_2="k_on"/>
<map_variables variable_1="k_off_C" variable_2="k_off_C"/>
<map_variables variable_1="k_off_O" variable_2="k_off_O"/>
<map_variables variable_1="P_NCX" variable_2="P_NCX"/>
<map_variables variable_1="K_mCa" variable_2="K_mCa"/>
<map_variables variable_1="K_mNai" variable_2="K_mNai"/>
<map_variables variable_1="k_sat" variable_2="k_sat"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="P_NaK" variable_2="P_NaK"/>
<map_variables variable_1="K_mK" variable_2="K_mK"/>
<map_variables variable_1="K_mNa" variable_2="K_mNa"/>
</connection>
<!-- We connect the initial conditions through to the model-->
<connection>
<map_components component_1="initial_conditions" component_2="Clamped_current"/>
<map_variables variable_1="Cai_total_init" variable_2="Cai_total_init"/>
<map_variables variable_1="Cai_init" variable_2="Cai_init"/>
<map_variables variable_1="Ki_init" variable_2="Ki_init"/>
<map_variables variable_1="Nai_init" variable_2="Nai_init"/>
<map_variables variable_1="O_CaL_init" variable_2="O_CaL_init"/>
<map_variables variable_1="C0_init" variable_2="C0_init"/>
<map_variables variable_1="C1_init" variable_2="C1_init"/>
<map_variables variable_1="C2_init" variable_2="C2_init"/>
<map_variables variable_1="C3_init" variable_2="C3_init"/>
<map_variables variable_1="C0Ca_init" variable_2="C0Ca_init"/>
<map_variables variable_1="C1Ca_init" variable_2="C1Ca_init"/>
<map_variables variable_1="C2Ca_init" variable_2="C2Ca_init"/>
<map_variables variable_1="C3Ca_init" variable_2="C3Ca_init"/>
<map_variables variable_1="ICa_init" variable_2="ICa_init"/>
<map_variables variable_1="IVs_init" variable_2="IVs_init"/>
<map_variables variable_1="IVf_init" variable_2="IVf_init"/>
<map_variables variable_1="IVfCa_init" variable_2="IVfCa_init"/>
<map_variables variable_1="IVsCa_init" variable_2="IVsCa_init"/>
<map_variables variable_1="d_CaT_init" variable_2="d_CaT_init"/>
<map_variables variable_1="f_CaT_init" variable_2="f_CaT_init"/>
<map_variables variable_1="x_Kv_init" variable_2="x_Kv_init"/>
<map_variables variable_1="y_Kv_init" variable_2="y_Kv_init"/>
<map_variables variable_1="BK_C0_init" variable_2="BK_C0_init"/>
<map_variables variable_1="BK_C1_init" variable_2="BK_C1_init"/>
<map_variables variable_1="BK_C2_init" variable_2="BK_C2_init"/>
<map_variables variable_1="BK_C3_init" variable_2="BK_C3_init"/>
<map_variables variable_1="BK_C4_init" variable_2="BK_C4_init"/>
<map_variables variable_1="O0_init" variable_2="O0_init"/>
<map_variables variable_1="O1_init" variable_2="O1_init"/>
<map_variables variable_1="O2_init" variable_2="O2_init"/>
<map_variables variable_1="O3_init" variable_2="O3_init"/>
<map_variables variable_1="O4_init" variable_2="O4_init"/>
<map_variables variable_1="Na_C1_init" variable_2="Na_C1_init"/>
<map_variables variable_1="Na_C2_init" variable_2="Na_C2_init"/>
<map_variables variable_1="Na_C3_init" variable_2="Na_C3_init"/>
<map_variables variable_1="I1_init" variable_2="I1_init"/>
<map_variables variable_1="I2_init" variable_2="I2_init"/>
<map_variables variable_1="O_Na_init" variable_2="O_Na_init"/>
</connection>
</model>
