- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-06-30 14:25:17+12:00
- Desc:
- Renaming Siekmann files to nondefault; using DeYoung instead
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/8ab/rawfile/e96fcf69494a24946ba1e4aad50ee4991d8e92e9/BG_IPR_Siekmann.cellml
<?xml version='1.0' encoding='UTF-8'?>
<!-- Siekmann 2012 model of the IPR.
NOTE for transition q_24 and q_42, dependence on Ca and IP3 concentrations have been neglected.
Rates are replaced with constant parameters.-->
<model name="individual_IPR" 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="units_and_constants/units_BG.cellml">
<units name="mM" units_ref="mM"/>
<units name="fmol" units_ref="fmol"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="microm3" units_ref="microm3"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="fA" units_ref="fA"/>
<units name="per_second" units_ref="per_second"/>
<units name="millivolt" units_ref="millivolt"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial values-->
<variable initial_value="0.007540192" name="q_Ca_i" public_interface="out" units="fmol"/>
<variable initial_value="0.763997897" name="q_Ca_SR" public_interface="out" units="fmol"/>
<variable initial_value="5.16E-03" name="q_IP3" public_interface="out" units="fmol"/>
<variable initial_value="1.6667e-4" name="q_C1" public_interface="out" units="fmol"/>
<variable initial_value="1.6667e-4" name="q_C2" public_interface="out" units="fmol"/>
<variable initial_value="1.6667e-4" name="q_C3" public_interface="out" units="fmol"/>
<variable initial_value="1.6667e-4" name="q_C4" public_interface="out" units="fmol"/>
<variable initial_value="1.6667e-4" name="q_O5" public_interface="out" units="fmol"/>
<variable initial_value="1.6667e-4" name="q_O6" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_R_IPR" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R12" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R23" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R24" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R26" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R45" public_interface="in" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_i</ci>
</apply>
<ci>v_R_IPR</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_SR</ci>
</apply>
<apply>
<minus/>
<ci>v_R_IPR</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_IP3</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
</math>
</component>
<component name="IPR_parameters">
<variable initial_value="0.135721" name="kappa_R_IPR" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.627589" name="kappa_R12" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0213951" name="kappa_R23" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.06975" name="kappa_R24" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="74.8828" name="kappa_R26" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="117673" name="kappa_R45" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0993" name="K_Ca_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0993" name="K_Ca_SR" public_interface="out" units="per_fmol"/>
<variable initial_value="0.269542" name="K_IP3" public_interface="out" units="per_fmol"/>
<variable initial_value="1975.81" name="K_C1" public_interface="out" units="per_fmol"/>
<variable initial_value="140.219" name="K_C2" public_interface="out" units="per_fmol"/>
<variable initial_value="3225.04" name="K_C3" public_interface="out" units="per_fmol"/>
<variable initial_value="9.34794e-05" name="K_C4" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0282988" name="K_O5" public_interface="out" units="per_fmol"/>
<variable initial_value="53.5503" name="K_O6" public_interface="out" units="per_fmol"/>
</component>
<component name="IPR">
<variable name="time" public_interface="in" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- parameters-->
<variable name="kappa_R_IPR" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R12" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R23" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R24" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R26" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R45" public_interface="in" units="fmol_per_sec"/>
<variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_SR" public_interface="in" units="per_fmol"/>
<variable name="K_IP3" public_interface="in" units="per_fmol"/>
<variable name="K_C1" public_interface="in" units="per_fmol"/>
<variable name="K_C2" public_interface="in" units="per_fmol"/>
<variable name="K_C3" public_interface="in" units="per_fmol"/>
<variable name="K_C4" public_interface="in" units="per_fmol"/>
<variable name="K_O5" public_interface="in" units="per_fmol"/>
<variable name="K_O6" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_Ca_i" public_interface="in" units="fmol"/>
<variable name="q_Ca_SR" public_interface="in" units="fmol"/>
<variable name="q_IP3" public_interface="in" units="fmol"/>
<variable name="q_C1" public_interface="in" units="fmol"/>
<variable name="q_C2" public_interface="in" units="fmol"/>
<variable name="q_C3" public_interface="in" units="fmol"/>
<variable name="q_C4" public_interface="in" units="fmol"/>
<variable name="q_O5" public_interface="in" units="fmol"/>
<variable name="q_O6" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_Ca_i" units="J_per_mol"/>
<variable name="mu_Ca_SR" units="J_per_mol"/>
<variable name="mu_IP3" units="J_per_mol"/>
<variable name="mu_C1" units="J_per_mol"/>
<variable name="mu_C2" units="J_per_mol"/>
<variable name="mu_C3" units="J_per_mol"/>
<variable name="mu_C4" units="J_per_mol"/>
<variable name="mu_O5" units="J_per_mol"/>
<variable name="mu_O6" units="J_per_mol"/>
<variable name="mu_open" units="J_per_mol"/>
<variable name="v_R_IPR" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R12" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R23" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R24" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R26" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R45" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_Ca_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_i</ci>
<ci>q_Ca_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Ca_SR</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_SR</ci>
<ci>q_Ca_SR</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_IP3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_IP3</ci>
<ci>q_IP3</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_C1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_C1</ci>
<ci>q_C1</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_C2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_C2</ci>
<ci>q_C2</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_C3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_C3</ci>
<ci>q_C3</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_C4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_C4</ci>
<ci>q_C4</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_O5</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_O5</ci>
<ci>q_O5</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_O6</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_O6</ci>
<ci>q_O6</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_open</ci>
<apply>
<plus/>
<ci>mu_O5</ci>
<ci>mu_O6</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_IPR</ci>
<apply>
<times/>
<ci>kappa_R_IPR</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_Ca_SR</ci>
<ci>mu_open</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_Ca_i</ci>
<ci>mu_open</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R12</ci>
<apply>
<times/>
<ci>kappa_R12</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R23</ci>
<apply>
<times/>
<ci>kappa_R23</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R24</ci>
<apply>
<times/>
<ci>kappa_R24</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R26</ci>
<apply>
<times/>
<ci>kappa_R26</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_O6</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R45</ci>
<apply>
<times/>
<ci>kappa_R45</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_O5</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_C1</ci>
</apply>
<apply>
<minus/>
<ci>v_R12</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_C2</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>v_R12</ci>
<ci>v_R23</ci>
</apply>
<ci>v_R24</ci>
</apply>
<ci>v_R26</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_C3</ci>
</apply>
<ci>v_R23</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_C4</ci>
</apply>
<apply>
<minus/>
<ci>v_R24</ci>
<ci>v_R45</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_O5</ci>
</apply>
<ci>v_R45</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_O6</ci>
</apply>
<ci>v_R26</ci>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="IPR"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_Ca_SR" variable_2="q_Ca_SR"/>
<map_variables variable_1="q_IP3" variable_2="q_IP3"/>
<map_variables variable_1="q_C1" variable_2="q_C1"/>
<map_variables variable_1="q_C2" variable_2="q_C2"/>
<map_variables variable_1="q_C3" variable_2="q_C3"/>
<map_variables variable_1="q_C4" variable_2="q_C4"/>
<map_variables variable_1="q_O5" variable_2="q_O5"/>
<map_variables variable_1="q_O6" variable_2="q_O6"/>
<map_variables variable_1="v_R_IPR" variable_2="v_R_IPR"/>
<map_variables variable_1="v_R12" variable_2="v_R12"/>
<map_variables variable_1="v_R23" variable_2="v_R23"/>
<map_variables variable_1="v_R24" variable_2="v_R24"/>
<map_variables variable_1="v_R26" variable_2="v_R26"/>
<map_variables variable_1="v_R45" variable_2="v_R45"/>
</connection>
<connection>
<map_components component_1="IPR" component_2="IPR_parameters"/>
<map_variables variable_1="kappa_R_IPR" variable_2="kappa_R_IPR"/>
<map_variables variable_1="kappa_R12" variable_2="kappa_R12"/>
<map_variables variable_1="kappa_R23" variable_2="kappa_R23"/>
<map_variables variable_1="kappa_R24" variable_2="kappa_R24"/>
<map_variables variable_1="kappa_R26" variable_2="kappa_R26"/>
<map_variables variable_1="kappa_R45" variable_2="kappa_R45"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_Ca_SR" variable_2="K_Ca_SR"/>
<map_variables variable_1="K_IP3" variable_2="K_IP3"/>
<map_variables variable_1="K_C1" variable_2="K_C1"/>
<map_variables variable_1="K_C2" variable_2="K_C2"/>
<map_variables variable_1="K_C3" variable_2="K_C3"/>
<map_variables variable_1="K_C4" variable_2="K_C4"/>
<map_variables variable_1="K_O5" variable_2="K_O5"/>
<map_variables variable_1="K_O6" variable_2="K_O6"/>
</connection>
<connection>
<map_components component_1="constants" component_2="IPR"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
