- 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/ASignallingExample.cellml
<?xml version="1.0" encoding="utf-8"?>
<model xmlns:xlink="http://www.w3.org/1999/xlink" name="ASignallingExample" cmeta:id="ASignallingExample" 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="per_m" units_ref="per_m"/>
<units name="per_m2" units_ref="per_m2"/>
<units name="N_per_m2" units_ref="N_per_m2"/>
<units name="m2_per_N" units_ref="m2_per_N"/>
<units name="N_per_m" units_ref="N_per_m"/>
<units name="N_m_per_K" units_ref="N_m_per_K"/>
<units name="uM" units_ref="uM"/>
<units name="uM_per_s" units_ref="uM_per_s"/>
<units name="per_uM_per_s" units_ref="per_uM_per_s"/>
</import>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Time.cellml">
<component name="Time" component_ref="Time"/>
</import>
<component name="environment_parameters">
<variable name="Ca_ext" units="uM" initial_value="2000" public_interface="out"/>
<variable name="tau" units="N_per_m2" initial_value="10" public_interface="out"/>
<variable name="T" units="kelvin" initial_value="310" public_interface="out"/>
</component>
<component name="cell_geometry_parameters">
<variable name="V_ce" units="dimensionless" initial_value="3.5" public_interface="out"/>
<variable name="l" units="meter" initial_value="3.5e-5" public_interface="out"/>
</component>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="ShearStress_to_IP3_Parameters.cellml">
<component name="ShearStress_to_IP3_Parameters" component_ref="ShearStress_to_IP3_Parameters"/>
</import>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="ShearStress_to_IP3.cellml">
<component name="ShearStress_to_IP3" component_ref="ShearStress_to_IP3"/>
</import>
<connection>
<map_components component_1="ShearStress_to_IP3_Parameters" component_2="ShearStress_to_IP3"/>
<map_variables variable_1="tau_c" variable_2="tau_c"/>
<map_variables variable_1="Rtau_phi_max" variable_2="Rtau_phi_max" />
<map_variables variable_1="Rtau_phi_init" variable_2="Rtau_phi_init" />
<map_variables variable_1="beta_phi" variable_2="beta_phi" />
<map_variables variable_1="Rtau_init" variable_2="Rtau_init" />
<map_variables variable_1="Rtau_k1" variable_2="Rtau_k1" />
<map_variables variable_1="Rtau_k2" variable_2="Rtau_k2" />
<map_variables variable_1="IP3_k1_init" variable_2="IP3_k1_init" />
<map_variables variable_1="IP3_k1_max" variable_2="IP3_k1_max" />
<map_variables variable_1="beta_IP3_k1" variable_2="beta_IP3_k1" />
<map_variables variable_1="IP3_k2_init" variable_2="IP3_k2_init" />
<map_variables variable_1="IP3_k2_max" variable_2="IP3_k2_max" />
<map_variables variable_1="beta_IP3_k2" variable_2="beta_IP3_k2" />
<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" />
<map_variables variable_1="IP3_init" variable_2="IP3_init" />
<map_variables variable_1="J_IP3_External" variable_2="J_IP3_External" />
</connection>
<connection>
<map_components component_1="environment_parameters" component_2="ShearStress_to_IP3"/>
<map_variables variable_1="tau" variable_2="tau"/>
</connection>
<connection>
<map_components component_1="Time" component_2="ShearStress_to_IP3"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="Calcium_Handling"/>
<map_variables variable_1="Ca_i" variable_2="Ca_if"/>
</connection>
<connection>
<map_components component_1="ShearStress_to_IP3" component_2="Calcium_Handling_Parameters"/>
<map_variables variable_1="Ca_i0" variable_2="Ca_if_rest"/>
</connection>
<component name="IP3_scaling_parameters">
<variable name="IP3_scalefactor" units="uM" initial_value="0.5" public_interface="out"/>
</component>
<component name="IP3_dimensionless_to_uM">
<variable name="IP3nd" units="dimensionless" public_interface="in"/>
<variable name="IP3_s" units="uM" public_interface="in"/>
<variable name="IP3" units="uM" public_interface="out"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>IP3</ci>
<apply>
<times/>
<ci>IP3nd</ci>
<ci>IP3_s</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="IP3_scaling_parameters" component_2="IP3_dimensionless_to_uM"/>
<map_variables variable_1="IP3_scalefactor" variable_2="IP3_s"/>
</connection>
<connection>
<map_components component_1="IP3_dimensionless_to_uM" component_2="ShearStress_to_IP3"/>
<map_variables variable_1="IP3nd" variable_2="IP3"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Calcium_Handling_Parameters.cellml">
<component name="Calcium_Handling_Parameters" component_ref="Calcium_Handling_Parameters"/>
</import>
<connection>
<map_components component_1="Calcium_Handling" component_2="Calcium_Handling_Parameters"/>
<map_variables variable_1="Ca_if_init" variable_2="Ca_if_init"/>
<map_variables variable_1="Ca_st_init" variable_2="Ca_st_init"/>
<map_variables variable_1="Ca_st_rest" variable_2="Ca_st_rest"/>
<map_variables variable_1="Ca_if_rest" variable_2="Ca_if_rest"/>
<map_variables variable_1="qout_basal_vmax" variable_2="qout_basal_vmax"/>
<map_variables variable_1="qout_basal_Km" variable_2="qout_basal_Km"/>
<map_variables variable_1="qout_basal_n" variable_2="qout_basal_n" />
<map_variables variable_1="qout_pump_vmax" variable_2="qout_pump_vmax"/>
<map_variables variable_1="qout_pump_Km" variable_2="qout_pump_Km"/>
<map_variables variable_1="qout_pump_n" variable_2="qout_pump_n"/>
<map_variables variable_1="qout_exch_vmax" variable_2="qout_exch_vmax"/>
<map_variables variable_1="qout_exch_Km" variable_2="qout_exch_Km"/>
<map_variables variable_1="qout_exch_n" variable_2="qout_exch_n"/>
<map_variables variable_1="qrel_k2" variable_2="qrel_k2"/>
<map_variables variable_1="qrel_k1" variable_2="qrel_k1"/>
<map_variables variable_1="qres_k1" variable_2="qres_k1"/>
<map_variables variable_1="qres_k2" variable_2="qres_k2"/>
<map_variables variable_1="qres_k3" variable_2="qres_k3"/>
<map_variables variable_1="qin_kcce" variable_2="qin_kcce" />
<map_variables variable_1="qin_max" variable_2="qin_max" />
<map_variables variable_1="qin_alpha" variable_2="qin_alpha"/>
<map_variables variable_1="qinw_f" variable_2="qinw_f" />
<map_variables variable_1="epsilon" variable_2="epsilon" />
<map_variables variable_1="k" variable_2="k" />
<map_variables variable_1="cac" variable_2="cac" />
<map_variables variable_1="qinw_delta" variable_2="qinw_delta"/>
<map_variables variable_1="J_Ca_st_External" variable_2="J_Ca_st_External"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Calcium_Handling.cellml">
<component name="Calcium_Handling" component_ref="Calcium_Handling"/>
</import>
<connection>
<map_components component_1="Calcium_Handling" component_2="environment_parameters"/>
<map_variables variable_1="Ca_ex" variable_2="Ca_ext"/>
<map_variables variable_1="tau" variable_2="tau"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
<connection>
<map_components component_1="Calcium_Handling" component_2="cell_geometry_parameters"/>
<map_variables variable_1="V_ce" variable_2="V_ce"/>
<map_variables variable_1="l" variable_2="l"/>
</connection>
<connection>
<map_components component_1="Calcium_Handling" component_2="IP3_dimensionless_to_uM"/>
<map_variables variable_1="IP3" variable_2="IP3"/>
</connection>
<connection>
<map_components component_1="Time" component_2="Calcium_Handling"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Calmodulin_Activation_Parameters.cellml">
<component name="Calmodulin_Activation_Parameters" component_ref="Calmodulin_Activation_Parameters"/>
</import>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Calmodulin_Activation.cellml">
<component name="Calmodulin_Activation" component_ref="Calmodulin_Activation"/>
</import>
<connection>
<map_components component_1="Calmodulin_Activation" component_2="Calmodulin_Activation_Parameters"/>
<map_variables variable_1="kon" variable_2="kon"/>
<map_variables variable_1="koff" variable_2="koff"/>
<map_variables variable_1="CaM_init" variable_2="CaM_init"/>
<map_variables variable_1="CaM_star_init" variable_2="CaM_star_init"/>
<map_variables variable_1="J_CaM_External" variable_2="J_CaM_External"/>
<map_variables variable_1="J_CaM_star_External" variable_2="J_CaM_star_External"/>
</connection>
<connection>
<map_components component_1="Calmodulin_Activation" component_2="Calcium_Handling"/>
<map_variables variable_1="Ca" variable_2="Ca_if"/>
</connection>
<connection>
<map_components component_1="Calmodulin_Activation" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<component name="Calmodulin_derived_Ca_buffering_outflux">
<variable name="J_Ca_buffering_outflux" units="uM_per_s" public_interface="out"/>
<variable name="J_CaM_star" units="uM_per_s" public_interface="in"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_Ca_buffering_outflux</ci>
<apply>
<times/>
<ci>J_CaM_star</ci>
<cn cellml:units="dimensionless">-4</cn>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="Calmodulin_derived_Ca_buffering_outflux" component_2="Calcium_Handling"/>
<map_variables variable_1="J_Ca_buffering_outflux" variable_2="J_Ca_if_External"/>
</connection>
<connection>
<map_components component_1="Calmodulin_derived_Ca_buffering_outflux" component_2="Calmodulin_Activation"/>
<map_variables variable_1="J_CaM_star" variable_2="J_CaM_star"/>
</connection>
</model>
