- Author:
- Michael Cooling <mcoo001@UoA.auckland.ac.nz>
- Date:
- 2016-04-11 12:30:41+12:00
- Desc:
- Adding .zip of complete model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/2c4/rawfile/ad404d66f734c5e175dca6c4601b7a2f00d8a1a3/ShearStress_to_IP3.cellml
<?xml version="1.0" encoding="utf-8"?>
<model xmlns:xlink="http://www.w3.org/1999/xlink" name="ShearStress_to_IP3" cmeta:id="ShearStress_to_IP3" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Units_Cellular_Systems.cellml">
<units name="per_s" units_ref="per_s"/>
<units name="N_per_m2" units_ref="N_per_m2"/>
<units name="m2_per_N" units_ref="m2_per_N"/>
<units name="uM" units_ref="uM"/>
</import>
<group>
<relationship_ref relationship="encapsulation" />
<component_ref component="ShearStress_to_IP3">
<component_ref component="tau_factor" />
<component_ref component="Rtau_phi" />
<component_ref component="Rtau_activation_factor" />
<component_ref component="R" />
<component_ref component="RtauActivation" />
<component_ref component="Rtau" />
<component_ref component="IP3_inactivation_factor" />
<component_ref component="IP3_k1" />
<component_ref component="IP3_k2" />
<component_ref component="IP3_generation_factor" />
<component_ref component="IP3Generation" />
<component_ref component="IP3" />
<component_ref component="IP3_delta" />
</component_ref>
</group>
<component name="ShearStress_to_IP3">
<variable name="time" units="second" public_interface="in" private_interface="out"/>
<variable name="tau" units="N_per_m2" public_interface="in" private_interface="out"/>
<variable name="tau_c" units="N_per_m2" public_interface="in" private_interface="out"/>
<variable name="Rtau_phi_max" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Rtau_phi_init" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="beta_phi" units="m2_per_N" public_interface="in" private_interface="out"/>
<variable name="Rtau_init" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Rtau_k1" units="per_s" public_interface="in" private_interface="out"/>
<variable name="Rtau_k2" units="per_s" public_interface="in" private_interface="out"/>
<variable name="IP3_k1_init" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="IP3_k1_max" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="beta_IP3_k1" units="m2_per_N" public_interface="in" private_interface="out"/>
<variable name="IP3_k2_init" units="per_s" public_interface="in" private_interface="out"/>
<variable name="IP3_k2_max" units="per_s" public_interface="in" private_interface="out"/>
<variable name="beta_IP3_k2" units="m2_per_N" public_interface="in" private_interface="out"/>
<variable name="Ca_i" units="uM" public_interface="in" private_interface="out"/>
<variable name="Ca_i0" units="uM" public_interface="in" private_interface="out"/>
<variable name="IP3_f_k1" units="per_s" public_interface="in" private_interface="out"/>
<variable name="IP3_f_k2" units="per_s" public_interface="in" private_interface="out"/>
<variable name="IP3_f_Km" units="uM" public_interface="in" private_interface="out"/>
<variable name="IP3_f_init" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="IP3_init" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="IP3" units="dimensionless" public_interface="out" private_interface="in"/>
<variable name="Rtau" units="dimensionless" public_interface="out" private_interface="in"/>
<variable name="J_IP3_External" units="per_s" public_interface="in" private_interface="out"/>
<variable name="J_IP3" units="per_s" public_interface="out" private_interface="in"/>
</component>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="IP3_delta"/>
<map_variables variable_1="J_IP3" variable_2="JNet"/>
</connection>
<component name="tau_factor">
<variable name="tau" units="N_per_m2" public_interface="in"/>
<variable name="tau_c" units="N_per_m2" public_interface="in"/>
<variable name="tau_factor" units="N_per_m2" public_interface="out"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>tau_factor</ci>
<piecewise>
<piece>
<cn cellml:units="N_per_m2">0</cn>
<apply>
<lt/>
<ci>tau</ci>
<ci>tau_c</ci>
</apply>
</piece>
<otherwise>
<apply>
<minus/>
<ci>tau</ci>
<ci>tau_c</ci>
</apply>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<connection>
<map_components component_1="tau_factor" component_2="ShearStress_to_IP3"/>
<map_variables variable_1="tau" variable_2="tau"/>
<map_variables variable_1="tau_c" variable_2="tau_c"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Bernoulli_dimensionless.cellml">
<component name="Rtau_phi" component_ref="Template_Bernoulli_dimensionless"/>
</import>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="Rtau_phi"/>
<map_variables variable_1="Rtau_phi_init" variable_2="y_i"/>
<map_variables variable_1="beta_phi" variable_2="beta_y"/>
<map_variables variable_1="Rtau_phi_max" variable_2="y_max"/>
</connection>
<connection>
<map_components component_1="tau_factor" component_2="Rtau_phi"/>
<map_variables variable_1="tau_factor" variable_2="stress"/>
</connection>
<component name="Rtau_activation_factor">
<variable name="Rtau_k1" units="per_s" public_interface="in"/>
<variable name="Rtau_phi" units="dimensionless" public_interface="in"/>
<variable name="Rtau_activation_factor" units="per_s" public_interface="out"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Rtau_activation_factor</ci>
<apply>
<times/>
<ci>Rtau_phi</ci>
<ci>Rtau_k1</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="Rtau_activation_factor"/>
<map_variables variable_1="Rtau_k1" variable_2="Rtau_k1"/>
</connection>
<connection>
<map_components component_1="Rtau_phi" component_2="Rtau_activation_factor"/>
<map_variables variable_1="y" variable_2="Rtau_phi"/>
</connection>
<component name="R">
<variable name="R" units="dimensionless" public_interface="out"/>
<variable name="Rtau" units="dimensionless" public_interface="in"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>R</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>Rtau</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="R" component_2="Rtau"/>
<map_variables variable_1="Rtau" variable_2="amount"/>
</connection>
<connection>
<map_components component_1="R" component_2="RtauActivation"/>
<map_variables variable_1="R" variable_2="A"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1P1_dimensionless.cellml">
<component name="RtauActivation" component_ref="Template_RateEqR1P1_dimensionless"/>
</import>
<connection>
<map_components component_1="Rtau_activation_factor" component_2="RtauActivation"/>
<map_variables variable_1="Rtau_activation_factor" variable_2="ka"/>
</connection>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="RtauActivation"/>
<map_variables variable_1="Rtau_k2" variable_2="kb"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_dimensionless.cellml">
<component name="Rtau" component_ref="Template_Species_dimensionless"/>
</import>
<connection>
<map_components component_1="Rtau" component_2="RtauActivation"/>
<map_variables variable_1="JGain" variable_2="J"/>
<map_variables variable_1="amount" variable_2="B"/>
</connection>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="Rtau"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Rtau_init" variable_2="amountInitialValue"/>
<map_variables variable_1="Rtau" variable_2="amount"/>
</connection>
<component name="IP3_inactivation_factor">
<variable name="Ca_i" units="uM" public_interface="in"/>
<variable name="Ca_i0" units="uM" public_interface="in"/>
<variable name="IP3_f_k1" units="per_s" public_interface="in"/>
<variable name="IP3_f_k2" units="per_s" public_interface="in"/>
<variable name="IP3_f_Km" units="uM" public_interface="in"/>
<variable name="time" units="second" public_interface="in"/>
<variable name="IP3_f_init" units="dimensionless" public_interface="in"/>
<variable name="IP3_f" units="dimensionless" initial_value="IP3_f_init" public_interface="out" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>IP3_f</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>IP3_f_k1</ci>
<apply>
<minus/>
<ci>Ca_i</ci>
<ci>Ca_i0</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>Ca_i</ci>
<ci>Ca_i0</ci>
</apply>
<ci>IP3_f_Km</ci>
</apply>
</apply>
<apply>
<times/>
<ci>IP3_f_k2</ci>
<ci>IP3_f</ci>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="IP3_inactivation_factor"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
<map_variables variable_1="Ca_i0" variable_2="Ca_i0"/>
<map_variables variable_1="IP3_f_k1" variable_2="IP3_f_k1"/>
<map_variables variable_1="IP3_f_k2" variable_2="IP3_f_k2"/>
<map_variables variable_1="IP3_f_Km" variable_2="IP3_f_Km"/>
<map_variables variable_1="IP3_f_init" variable_2="IP3_f_init"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Bernoulli_dimensionless.cellml">
<component name="IP3_k1" component_ref="Template_Bernoulli_dimensionless"/>
</import>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="IP3_k1"/>
<map_variables variable_1="IP3_k1_init" variable_2="y_i"/>
<map_variables variable_1="beta_IP3_k1" variable_2="beta_y"/>
<map_variables variable_1="IP3_k1_max" variable_2="y_max"/>
</connection>
<connection>
<map_components component_1="tau_factor" component_2="IP3_k1"/>
<map_variables variable_1="tau_factor" variable_2="stress"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Bernoulli_per_s.cellml">
<component name="IP3_k2" component_ref="Template_Bernoulli_per_s"/>
</import>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="IP3_k2"/>
<map_variables variable_1="IP3_k2_init" variable_2="y_i"/>
<map_variables variable_1="beta_IP3_k2" variable_2="beta_y"/>
<map_variables variable_1="IP3_k2_max" variable_2="y_max"/>
</connection>
<connection>
<map_components component_1="tau_factor" component_2="IP3_k2"/>
<map_variables variable_1="tau_factor" variable_2="stress"/>
</connection>
<component name="IP3_generation_factor" >
<variable name="IP3_generation_factor" units="dimensionless" public_interface="out"/>
<variable name="IP3_k1" units="dimensionless" public_interface="in"/>
<variable name="IP3_f" units="dimensionless" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>IP3_generation_factor</ci>
<apply>
<times/>
<ci>IP3_k1</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>IP3_f</ci>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="IP3_generation_factor" component_2="IP3_k1"/>
<map_variables variable_1="IP3_k1" variable_2="y"/>
</connection>
<connection>
<map_components component_1="IP3_generation_factor" component_2="IP3_inactivation_factor"/>
<map_variables variable_1="IP3_f" variable_2="IP3_f"/>
</connection>
<connection>
<map_components component_1="IP3_generation_factor" component_2="IP3Generation"/>
<map_variables variable_1="IP3_generation_factor" variable_2="A"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1P1_dimensionless.cellml">
<component name="IP3Generation" component_ref="Template_RateEqR1P1_dimensionless"/>
</import>
<connection>
<map_components component_1="RtauActivation" component_2="IP3Generation"/>
<map_variables variable_1="J" variable_2="ka"/>
</connection>
<connection>
<map_components component_1="IP3_k2" component_2="IP3Generation"/>
<map_variables variable_1="y" variable_2="kb"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_dimensionless.cellml">
<component name="IP3" component_ref="Template_Species_dimensionless"/>
</import>
<connection>
<map_components component_1="IP3" component_2="IP3Generation"/>
<map_variables variable_1="amount" variable_2="B"/>
</connection>
<connection>
<map_components component_1="IP3" component_2="IP3_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="IP3"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="IP3_init" variable_2="amountInitialValue"/>
<map_variables variable_1="IP3" variable_2="amount"/>
</connection>
<component name="IP3_delta">
<variable name="JPlusGeneration" units="per_s" public_interface="in" />
<variable name="JPlusExternal" units="per_s" public_interface="in" />
<variable name="JNet" units="per_s" public_interface="out" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<plus/>
<ci>JPlusGeneration</ci>
<ci>JPlusExternal</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="IP3_delta" component_2="IP3Generation"/>
<map_variables variable_1="JPlusGeneration" variable_2="J"/>
</connection>
<connection>
<map_components component_1="IP3_delta" component_2="ShearStress_to_IP3"/>
<map_variables variable_1="JPlusExternal" variable_2="J_IP3_External"/>
</connection>
</model>
