- Author:
- Michael Cooling <mcoo001@UoA.auckland.ac.nz>
- Date:
- 2016-04-11 12:26:19+12:00
- Desc:
- Adding .zip file of complete model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/2c5/rawfile/cce6374c21a60771321701b2f88857175ca5c31e/ACoreDomainsExample.cellml
<?xml version="1.0" encoding="utf-8"?>
<model xmlns:xlink="http://www.w3.org/1999/xlink" name="ACoreDomainsExample" cmeta:id="ACoreDomainsExample" 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/Time.cellml">
<component name="Time" component_ref="Time"/>
</import>
<import xlink:href="Principled_Base/mohr_taylor_newell_2008_subset.cellml">
<units name="J_per_mole_per_K" units_ref="J_per_mole_per_K" />
<units name="C_per_mole" units_ref="C_per_mole" />
<units name="per_mole" units_ref="per_mole" />
<component name="codata_2006_physicochemical" component_ref="codata_2006_physicochemical_subset" />
</import>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="codata_2006_physicochemical"/>
<map_variables variable_1="R" variable_2="molar_gas_constant" />
<map_variables variable_1="F" variable_2="Faraday_constant" />
<map_variables variable_1="avogadrosConstant" variable_2="Avogadro_constant"/>
</connection>
<component name="ACoreDomainsExample_Parameters">
<variable name="stimTime" public_interface="out" initial_value="50000" units="ms"/>
<variable name="stimDuration" public_interface="out" initial_value="100" units="ms"/>
<variable name="stimCurrent" public_interface="out" initial_value="-5" units="uA_per_mm3"/>
<variable name="Am" public_interface="out" initial_value="200" units="per_mm"/>
<variable name="Cm" units="uF_per_mm2" public_interface="out" initial_value="0.01"/>
<variable name="V_init" units="mV" public_interface="out" initial_value="-120"/>
<variable name="vC" units="dimensionless" public_interface="out" initial_value="0.49"/>
<variable name="H_init" units="mM" initial_value="6.31e-5" public_interface="out"/>
<variable name="ATP_init" units="mM" initial_value="6.8" public_interface="out"/>
<variable name="k_half_pHi" units="mM" initial_value="0.265e-3" public_interface="out"/>
<variable name="H_o" units="mM" initial_value="3.98e-5" public_interface="out"/>
<variable name="k_half_pHo" units="mM" initial_value="3.162e-3" public_interface="out"/>
<variable name="k_half_ATPi" units="mM" initial_value="1.4" public_interface="out"/>
<variable name="H_ATPi" units="dimensionless" initial_value="2.6" public_interface="out"/>
<variable name="g_CaL" units="mm_per_ms" initial_value="1.75e-6" public_interface="out" />
<variable name="Cai_init" units="mM" public_interface="out" initial_value="0.0007"/>
<variable name="Cao" units="mM" public_interface="out" initial_value="2.0" />
<variable name="T" units="K" public_interface="out" initial_value="310" />
<variable name="d_init" initial_value="0.0" units="dimensionless" public_interface="out"/>
<variable name="f_init" initial_value="1.0" units="dimensionless" public_interface="out"/>
<variable name="fCa_init" initial_value="1.0" units="dimensionless" public_interface="out"/>
<variable name="I_V_MinusExternal" public_interface="out" initial_value="0" units="uA_per_mm2" />
<variable name="J_Cai_External" public_interface="out" initial_value="0" units="mM_per_s" />
<variable name="ADP_init" units="M" initial_value="0" public_interface="out"/>
<variable name="Pi_init" units="M" initial_value="0" public_interface="out" />
<variable name="Mg_init" units="M" initial_value="1e-3" public_interface="out" />
<variable name="K_init" units="M" initial_value="1.5e-1" public_interface="out" />
<variable name="BX" units="M" initial_value="0" public_interface="out"/>
<variable name="K_BX" units="M" initial_value="1e-7" public_interface="out"/>
<variable name="ATPASE_p1" units="per_s" initial_value="0" public_interface="out"/>
<variable name="Env" units="dimensionless" initial_value="2.562" public_interface="out"/>
<variable name="Kh1" units="dimensionless" initial_value="2.8e-7" public_interface="out"/>
<variable name="Km1" units="dimensionless" initial_value="0.000108" public_interface="out"/>
<variable name="Kk1" units="dimensionless" initial_value="0.0971" public_interface="out"/>
<variable name="Kh2" units="dimensionless" initial_value="4.19e-7" public_interface="out"/>
<variable name="Km2" units="dimensionless" initial_value="0.000882" public_interface="out"/>
<variable name="Kk2" units="dimensionless" initial_value="0.131" public_interface="out"/>
<variable name="Kh3" units="dimensionless" initial_value="2.13e-7" public_interface="out"/>
<variable name="Km3" units="dimensionless" initial_value="0.0321" public_interface="out"/>
<variable name="Kk3" units="dimensionless" initial_value="0.379" public_interface="out"/>
<variable name="DGro_ATPASE" units="dimensionless" initial_value="4.508" public_interface="out"/>
<variable name="J_H_External" units="M_per_s" initial_value="0" public_interface="out"/>
<variable name="J_ATP_External" units="M_per_s" initial_value="0" public_interface="out"/>
<variable name="J_ADP_External" units="M_per_s" initial_value="0" public_interface="out"/>
<variable name="J_Pi_External" units="M_per_s" initial_value="0" public_interface="out" />
<variable name="J_Mg_External" units="M_per_s" initial_value="0" public_interface="out" />
<variable name="J_K_External" units="M_per_s" initial_value="0" public_interface="out" />
<variable name="kon" units="per_uM_per_s" initial_value="0.1" public_interface="out"/>
<variable name="koff" units="per_s" initial_value="0.3" public_interface="out"/>
<variable name="CaM_init" units="uM" initial_value="2.04" public_interface="out"/>
<variable name="CaM_star_init" units="uM" initial_value="0.46" public_interface="out"/>
<variable name="J_CaM_External" units="uM_per_s" initial_value="0" public_interface="out"/>
<variable name="J_CaM_star_External" units="uM_per_s" initial_value="0" public_interface="out"/>
<variable name="Ccn" units="dimensionless" initial_value="50" public_interface="out"/>
<variable name="act_N" units="dimensionless" initial_value="0.9" public_interface="out"/>
<variable name="Ntot" units="nM" initial_value="1000" public_interface="out"/>
<variable name="K_mN" units="nM" public_interface="out" initial_value="1200"/>
<variable name="n" units="dimensionless" public_interface="out" initial_value="2.92"/>
<variable name="K_dN" units="nM" public_interface="out" initial_value="1760"/>
<variable name="k_f1" units="per_nM_per_s" initial_value="2e-3" public_interface="out"/>
<variable name="k_r1" units="per_s" initial_value="2e1" public_interface="out"/>
<variable name="k_f2" units="per_s" initial_value="1.5" public_interface="out"/>
<variable name="k_f3" units="per_s" initial_value="3.7e-1" public_interface="out"/>
<variable name="k_r3" units="per_nM_per_s" initial_value="4.7e-2" public_interface="out"/>
<variable name="k_f4" units="per_s" initial_value="4.4e-1" public_interface="out"/>
<variable name="NFATp_c_init" units="nM" initial_value="0.615" public_interface="out"/>
<variable name="NFATN_c_init" units="nM" initial_value="6.55e-3" public_interface="out"/>
<variable name="NFATN_n_init" units="nM" initial_value="17.6" public_interface="out"/>
<variable name="NFATp_n_init" units="nM" initial_value="1.10" public_interface="out"/>
<variable name="J_NFATp_c_External" units="nM_per_s" initial_value="0" public_interface="out"/>
<variable name="J_NFATN_c_External" units="nM_per_s" initial_value="0" public_interface="out"/>
<variable name="J_NFATN_n_External" units="nM_per_s" initial_value="0" public_interface="out"/>
<variable name="J_NFATp_n_External" units="nM_per_s" initial_value="0" public_interface="out"/>
<variable name="Promoter_GFP_k" units="PoPs" initial_value="8.0" public_interface="out" />
<variable name="Promoter_GFP_n" units="dimensionless" initial_value="2" public_interface="out"/>
<variable name="Promoter_GFP_Km" units="nM" initial_value="320" public_interface="out"/>
<variable name="transcriptionalVolume_init" units="femtoliter" initial_value="1" public_interface="out" />
<variable name="translationalVolume_init" units="femtoliter" initial_value="50" public_interface="out" />
<variable name="RNA_n_init" units="nM" initial_value="0" public_interface="out" />
<variable name="J_RNA_n_External" units="nM_per_s" initial_value="0" public_interface="out" />
<variable name="RNA_c_init" units="nM" initial_value="0" public_interface="out" />
<variable name="J_RNA_c_External" units="nM_per_s" initial_value="0" public_interface="out" />
<variable name="GFP_init" units="nM" initial_value="0" public_interface="out" />
<variable name="J_GFP_External" units="nM_per_s" initial_value="0" public_interface="out" />
<variable name="RNA_kDecay" units="per_s" initial_value="1e-4" public_interface="out" />
<variable name="RNA_Transport_k" units="per_s" initial_value="0.8" public_interface="out" />
<variable name="RBS_k" units="RiPs" initial_value="6.0" public_interface="out" />
<variable name="GFP_kDecay" units="per_s" initial_value="0.6" public_interface="out" />
</component>
<connection>
<map_components component_1="ACoreDomainsExample_Parameters" component_2="ACoreDomainsExample"/>
<map_variables variable_1="stimTime" variable_2="stimTime"/>
<map_variables variable_1="stimDuration" variable_2="stimDuration" />
<map_variables variable_1="stimCurrent" variable_2="stimCurrent" />
<map_variables variable_1="Am" variable_2="Am" />
<map_variables variable_1="Cm" variable_2="Cm" />
<map_variables variable_1="V_init" variable_2="V_init" />
<map_variables variable_1="vC" variable_2="vC" />
<map_variables variable_1="H_init" variable_2="H_init" />
<map_variables variable_1="ATP_init" variable_2="ATP_init" />
<map_variables variable_1="k_half_pHi" variable_2="k_half_pHi" />
<map_variables variable_1="H_o" variable_2="H_o" />
<map_variables variable_1="k_half_pHo" variable_2="k_half_pHo" />
<map_variables variable_1="k_half_ATPi" variable_2="k_half_ATPi" />
<map_variables variable_1="H_ATPi" variable_2="H_ATPi" />
<map_variables variable_1="g_CaL" variable_2="g_CaL" />
<map_variables variable_1="Cai_init" variable_2="Cai_init" />
<map_variables variable_1="Cao" variable_2="Cao" />
<map_variables variable_1="T" variable_2="T" />
<map_variables variable_1="d_init" variable_2="d_init" />
<map_variables variable_1="f_init" variable_2="f_init" />
<map_variables variable_1="fCa_init" variable_2="fCa_init" />
<map_variables variable_1="I_V_MinusExternal" variable_2="I_V_MinusExternal"/>
<map_variables variable_1="J_Cai_External" variable_2="J_Cai_External"/>
<map_variables variable_1="ADP_init" variable_2="ADP_init" />
<map_variables variable_1="Pi_init" variable_2="Pi_init" />
<map_variables variable_1="Mg_init" variable_2="Mg_init" />
<map_variables variable_1="K_init" variable_2="K_init" />
<map_variables variable_1="BX" variable_2="BX" />
<map_variables variable_1="K_BX" variable_2="K_BX" />
<map_variables variable_1="ATPASE_p1" variable_2="ATPASE_p1" />
<map_variables variable_1="Env" variable_2="Env" />
<map_variables variable_1="Kh1" variable_2="Kh1" />
<map_variables variable_1="Km1" variable_2="Km1" />
<map_variables variable_1="Kk1" variable_2="Kk1" />
<map_variables variable_1="Kh2" variable_2="Kh2" />
<map_variables variable_1="Km2" variable_2="Km2" />
<map_variables variable_1="Kk2" variable_2="Kk2" />
<map_variables variable_1="Kh3" variable_2="Kh3" />
<map_variables variable_1="Km3" variable_2="Km3" />
<map_variables variable_1="Kk3" variable_2="Kk3" />
<map_variables variable_1="DGro_ATPASE" variable_2="DGro_ATPASE"/>
<map_variables variable_1="J_ATP_External" variable_2="J_ATP_External" />
<map_variables variable_1="J_ADP_External" variable_2="J_ADP_External" />
<map_variables variable_1="J_H_External" variable_2="J_H_External" />
<map_variables variable_1="J_Pi_External" variable_2="J_Pi_External" />
<map_variables variable_1="J_Mg_External" variable_2="J_Mg_External" />
<map_variables variable_1="J_K_External" variable_2="J_K_External" />
<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="kon" variable_2="kon"/>
<map_variables variable_1="koff" variable_2="koff"/>
<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"/>
<map_variables variable_1="Ccn" variable_2="Ccn" />
<map_variables variable_1="Ntot" variable_2="Ntot" />
<map_variables variable_1="k_f1" variable_2="k_f1" />
<map_variables variable_1="k_r1" variable_2="k_r1" />
<map_variables variable_1="k_f2" variable_2="k_f2" />
<map_variables variable_1="k_f3" variable_2="k_f3" />
<map_variables variable_1="k_r3" variable_2="k_r3" />
<map_variables variable_1="k_f4" variable_2="k_f4" />
<map_variables variable_1="NFATp_c_init" variable_2="NFATp_c_init" />
<map_variables variable_1="NFATN_c_init" variable_2="NFATN_c_init" />
<map_variables variable_1="NFATN_n_init" variable_2="NFATN_n_init" />
<map_variables variable_1="NFATp_n_init" variable_2="NFATp_n_init" />
<map_variables variable_1="J_NFATp_c_External" variable_2="J_NFATp_c_External" />
<map_variables variable_1="J_NFATN_c_External" variable_2="J_NFATN_c_External" />
<map_variables variable_1="J_NFATN_n_External" variable_2="J_NFATN_n_External" />
<map_variables variable_1="J_NFATp_n_External" variable_2="J_NFATp_n_External" />
<map_variables variable_1="K_mN" variable_2="K_mN"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="K_dN" variable_2="K_dN"/>
<map_variables variable_1="Promoter_GFP_k" variable_2="Promoter_GFP_k" />
<map_variables variable_1="Promoter_GFP_n" variable_2="Promoter_GFP_n" />
<map_variables variable_1="Promoter_GFP_Km" variable_2="Promoter_GFP_Km" />
<map_variables variable_1="transcriptionalVolume_init" variable_2="transcriptionalVolume_init" />
<map_variables variable_1="translationalVolume_init" variable_2="translationalVolume_init" />
<map_variables variable_1="RNA_n_init" variable_2="RNA_n_init" />
<map_variables variable_1="J_RNA_n_External" variable_2="J_RNA_n_External" />
<map_variables variable_1="RNA_c_init" variable_2="RNA_c_init" />
<map_variables variable_1="J_RNA_c_External" variable_2="J_RNA_c_External" />
<map_variables variable_1="GFP_init" variable_2="GFP_init" />
<map_variables variable_1="J_GFP_External" variable_2="J_GFP_External" />
<map_variables variable_1="RNA_kDecay" variable_2="RNA_kDecay" />
<map_variables variable_1="RNA_Transport_k" variable_2="RNA_Transport_k" />
<map_variables variable_1="RBS_k" variable_2="RBS_k" />
<map_variables variable_1="GFP_kDecay" variable_2="GFP_kDecay" />
</connection>
<group>
<relationship_ref relationship="encapsulation" />
<component_ref component="ACoreDomainsExample">
<component_ref component="StimCurrent_SinglePulse" />
<component_ref component="ICaL_to_Cai" />
<component_ref component="membraneV_delta" />
<component_ref component="Myosin_ATPASE" />
<component_ref component="Calmodulin_Activation" />
<component_ref component="Cai_delta" />
<component_ref component="CaMActivation_Ca_J_Scaling" />
<component_ref component="CaN_to_DNAReady_NFAT" />
<component_ref component="ExampleDevice" />
</component_ref>
</group>
<component name="ACoreDomainsExample">
<variable name="stimTime" public_interface="in" private_interface="out" units="ms"/>
<variable name="stimDuration" public_interface="in" private_interface="out" units="ms"/>
<variable name="stimCurrent" public_interface="in" private_interface="out" units="uA_per_mm3"/>
<variable name="Am" public_interface="in" private_interface="out" units="per_mm"/>
<variable name="time" public_interface="in" private_interface="out" units="second"/>
<variable name="Cm" units="uF_per_mm2" public_interface="in" private_interface="out"/>
<variable name="V_init" units="mV" public_interface="in" private_interface="out"/>
<variable name="vC" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="H_init" units="mM" public_interface="in" private_interface="out"/>
<variable name="k_half_pHi" units="mM" public_interface="in" private_interface="out"/>
<variable name="H_o" units="mM" public_interface="in" private_interface="out"/>
<variable name="k_half_pHo" units="mM" public_interface="in" private_interface="out"/>
<variable name="ATP_init" units="mM" public_interface="in" private_interface="out"/>
<variable name="k_half_ATPi" units="mM" public_interface="in" private_interface="out"/>
<variable name="H_ATPi" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="g_CaL" public_interface="in" private_interface="out" units="mm_per_ms"/>
<variable name="Cai_init" public_interface="in" private_interface="out" units="mM"/>
<variable name="Cao" public_interface="in" private_interface="out" units="mM"/>
<variable name="T" public_interface="in" private_interface="out" units="K"/>
<variable name="R" public_interface="in" private_interface="out" units="J_per_mole_per_K"/>
<variable name="F" public_interface="in" private_interface="out" units="C_per_mole"/>
<variable name="d_init" public_interface="in" private_interface="out" units="dimensionless" />
<variable name="f_init" public_interface="in" private_interface="out" units="dimensionless" />
<variable name="fCa_init" public_interface="in" private_interface="out" units="dimensionless" />
<variable name="I_V_MinusExternal" public_interface="in" private_interface="out" units="uA_per_mm2" />
<variable name="J_Cai_External" public_interface="in" private_interface="out" units="mM_per_s" />
<variable name="ADP_init" units="M" public_interface="in" private_interface="out"/>
<variable name="Pi_init" units="M" public_interface="in" private_interface="out"/>
<variable name="Mg_init" units="M" public_interface="in" private_interface="out"/>
<variable name="K_init" units="M" public_interface="in" private_interface="out"/>
<variable name="BX" units="M" public_interface="in" private_interface="out"/>
<variable name="K_BX" units="M" public_interface="in" private_interface="out"/>
<variable name="ATPASE_p1" units="per_s" public_interface="in" private_interface="out"/>
<variable name="Env" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Kh1" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Km1" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Kk1" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Kh2" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Km2" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Kk2" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Kh3" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Km3" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Kk3" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="DGro_ATPASE" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="J_H_External" units="M_per_s" public_interface="in" private_interface="out"/>
<variable name="J_ATP_External" units="M_per_s" public_interface="in" private_interface="out"/>
<variable name="J_ADP_External" units="M_per_s" public_interface="in" private_interface="out"/>
<variable name="J_Pi_External" units="M_per_s" public_interface="in" private_interface="out"/>
<variable name="J_Mg_External" units="M_per_s" public_interface="in" private_interface="out"/>
<variable name="J_K_External" units="M_per_s" public_interface="in" private_interface="out"/>
<variable name="CaM_init" units="uM" public_interface="in" private_interface="out"/>
<variable name="CaM_star_init" units="uM" public_interface="in" private_interface="out"/>
<variable name="kon" units="per_uM_per_s" public_interface="in" private_interface="out"/>
<variable name="koff" units="per_s" public_interface="in" private_interface="out"/>
<variable name="J_CaM_External" units="uM_per_s" public_interface="in" private_interface="out" />
<variable name="J_CaM_star_External" units="uM_per_s" public_interface="in" private_interface="out" />
<variable name="CaMActivation_Ca_J_ScaleFactor" units="dimensionless" initial_value="4" private_interface="out" />
<variable name="K_mN" units="nM" public_interface="in" private_interface="out"/>
<variable name="n" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="K_dN" units="nM" public_interface="in" private_interface="out"/>
<variable name="Ccn" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Ntot" units="nM" public_interface="in" private_interface="out"/>
<variable name="k_f1" units="per_nM_per_s" public_interface="in" private_interface="out"/>
<variable name="k_r1" units="per_s" public_interface="in" private_interface="out"/>
<variable name="k_f2" units="per_s" public_interface="in" private_interface="out"/>
<variable name="k_f3" units="per_s" public_interface="in" private_interface="out"/>
<variable name="k_r3" units="per_nM_per_s" public_interface="in" private_interface="out"/>
<variable name="k_f4" units="per_s" public_interface="in" private_interface="out"/>
<variable name="NFATp_c_init" units="nM" private_interface="out" public_interface="in"/>
<variable name="NFATN_c_init" units="nM" private_interface="out" public_interface="in"/>
<variable name="NFATN_n_init" units="nM" private_interface="out" public_interface="in"/>
<variable name="NFATp_n_init" units="nM" private_interface="out" public_interface="in"/>
<variable name="J_NFATp_c_External" units="nM_per_s" private_interface="out" public_interface="in"/>
<variable name="J_NFATN_c_External" units="nM_per_s" private_interface="out" public_interface="in"/>
<variable name="J_NFATN_n_External" units="nM_per_s" private_interface="out" public_interface="in"/>
<variable name="J_NFATp_n_External" units="nM_per_s" private_interface="out" public_interface="in"/>
<variable name="I_V_Minus" public_interface="out" private_interface="in" units="uA_per_mm2" />
<variable name="V" public_interface="out" private_interface="in" units="mV"/>
<variable name="Cai" public_interface="out" private_interface="in" units="mM"/>
<variable name="J_Cai" public_interface="out" private_interface="in" units="mM_per_s"/>
<variable name="ATP" units="M" public_interface="out" private_interface="in"/>
<variable name="ADP" units="M" public_interface="out" private_interface="in"/>
<variable name="Pi" units="M" public_interface="out" private_interface="in"/>
<variable name="H" units="M" public_interface="out" private_interface="in"/>
<variable name="Mg" units="M" public_interface="out" private_interface="in"/>
<variable name="K" units="M" public_interface="out" private_interface="in"/>
<variable name="J_H" units="M_per_s" public_interface="out" private_interface="in"/>
<variable name="J_ATP" units="M_per_s" public_interface="out" private_interface="in"/>
<variable name="J_ADP" units="M_per_s" public_interface="out" private_interface="in"/>
<variable name="J_Pi" units="M_per_s" public_interface="out" private_interface="in"/>
<variable name="J_Mg" units="M_per_s" public_interface="out" private_interface="in"/>
<variable name="J_K" units="M_per_s" public_interface="out" private_interface="in"/>
<variable name="CaM" units="uM" public_interface="out" private_interface="in"/>
<variable name="J_CaM" units="uM_per_s" public_interface="out" private_interface="in"/>
<variable name="CaM_star" units="uM" public_interface="out" private_interface="in"/>
<variable name="J_CaM_star" units="uM_per_s" public_interface="out" private_interface="in"/>
<variable name="CaM_total" units="uM" private_interface="out" />
<variable name="avogadrosConstant" units="per_mole" public_interface="in" private_interface="out"/>
<variable name="Promoter_GFP_k" units="PoPs" public_interface="in" private_interface="out" />
<variable name="Promoter_GFP_n" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Promoter_GFP_Km" units="nM" public_interface="in" private_interface="out"/>
<variable name="transcriptionalVolume_init" units="femtoliter" public_interface="in" private_interface="out"/>
<variable name="translationalVolume_init" units="femtoliter" public_interface="in" private_interface="out"/>
<variable name="RNA_n_init" units="nM" public_interface="in" private_interface="out" />
<variable name="J_RNA_n_External" units="nM_per_s" public_interface="in" private_interface="out" />
<variable name="RNA_c_init" units="nM" public_interface="in" private_interface="out" />
<variable name="J_RNA_c_External" units="nM_per_s" public_interface="in" private_interface="out" />
<variable name="GFP_init" units="nM" public_interface="in" private_interface="out" />
<variable name="J_GFP_External" units="nM_per_s" public_interface="in" private_interface="out" />
<variable name="RNA_kDecay" units="per_s" public_interface="in" private_interface="out" />
<variable name="RNA_Transport_k" units="per_s" public_interface="in" private_interface="out" />
<variable name="RBS_k" units="RiPs" public_interface="in" private_interface="out" />
<variable name="GFP_kDecay" units="per_s" public_interface="in" private_interface="out" />
<variable name="N_active_ratio" units="dimensionless" private_interface="in" public_interface="out"/>
<variable name="NFATp_c" units="nM" private_interface="in" public_interface="out"/>
<variable name="NFATN_c" units="nM" private_interface="in" public_interface="out"/>
<variable name="NFATN_n" units="nM" private_interface="in" public_interface="out"/>
<variable name="NFATp_n" units="nM" private_interface="in" public_interface="out"/>
<variable name="J_NFATp_c" units="nM_per_s" private_interface="in" public_interface="out"/>
<variable name="J_NFATN_c" units="nM_per_s" private_interface="in" public_interface="out"/>
<variable name="J_NFATN_n" units="nM_per_s" private_interface="in" public_interface="out"/>
<variable name="J_NFATp_n" units="nM_per_s" private_interface="in" public_interface="out"/>
<variable name="J_RNA_n" units="nM_per_s" public_interface="out" private_interface="in" />
<variable name="RNA_n" units="nM" public_interface="out" private_interface="in"/>
<variable name="J_RNA_c" units="nM_per_s" public_interface="out" private_interface="in" />
<variable name="RNA_c" units="nM" public_interface="out" private_interface="in"/>
<variable name="transcriptionalVolume" units="femtoliter" public_interface="out" private_interface="in"/>
<variable name="translationalVolume" units="femtoliter" public_interface="out" private_interface="in"/>
<variable name="J_GFP" units="nM_per_s" public_interface="out" private_interface="in" />
<variable name="GFP" units="nM" public_interface="out" private_interface="in"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<ci>CaM_total</ci>
<apply>
<plus/>
<ci>CaM</ci>
<ci>CaM_star</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="Time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="StimCurrent_SinglePulse.cellml">
<units name="ms" units_ref="ms" />
<units name="uA_per_mm3" units_ref="uA_per_mm3" />
<component name="StimCurrent_SinglePulse" component_ref="StimCurrent_SinglePulse"/>
</import>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="StimCurrent_SinglePulse"/>
<map_variables variable_1="stimTime" variable_2="stimTime"/>
<map_variables variable_1="stimDuration" variable_2="stimDuration"/>
<map_variables variable_1="stimCurrent" variable_2="stimCurrent"/>
<map_variables variable_1="Am" variable_2="Am"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="ICaL_to_Cai.cellml">
<units name="per_ms" units_ref="per_ms" />
<units name="per_mm" units_ref="per_mm" />
<units name="uF_per_mm2" units_ref="uF_per_mm2" />
<units name="mV" units_ref="mV" />
<units name="mM" units_ref="mM" />
<units name="K" units_ref="K" />
<units name="uA_per_mm2" units_ref="uA_per_mm2" />
<units name="mm_per_ms" units_ref="mm_per_ms" />
<units name="mM_per_s" units_ref="mM_per_s" />
<component name="ICaL_to_Cai" component_ref="ICaL_to_Cai"/>
</import>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="ICaL_to_Cai"/>
<map_variables variable_1="time" variable_2="time" />
<map_variables variable_1="Cm" variable_2="Cm" />
<map_variables variable_1="V_init" variable_2="V_init" />
<map_variables variable_1="Am" variable_2="Am" />
<map_variables variable_1="vC" variable_2="vC" />
<map_variables variable_1="k_half_pHi" variable_2="k_half_pHi" />
<map_variables variable_1="H_o" variable_2="H_o" />
<map_variables variable_1="k_half_pHo" variable_2="k_half_pHo" />
<map_variables variable_1="k_half_ATPi" variable_2="k_half_ATPi" />
<map_variables variable_1="H_ATPi" variable_2="H_ATPi" />
<map_variables variable_1="g_CaL" variable_2="g_CaL" />
<map_variables variable_1="Cai_init" variable_2="Cai_init" />
<map_variables variable_1="Cao" variable_2="Cao" />
<map_variables variable_1="T" variable_2="T" />
<map_variables variable_1="F" variable_2="F" />
<map_variables variable_1="R" variable_2="R" />
<map_variables variable_1="d_init" variable_2="d_init" />
<map_variables variable_1="f_init" variable_2="f_init" />
<map_variables variable_1="fCa_init" variable_2="fCa_init" />
<map_variables variable_1="V" variable_2="V" />
<map_variables variable_1="Cai" variable_2="Cai" />
<map_variables variable_1="J_Cai" variable_2="J_Cai" />
<map_variables variable_1="I_V_Minus" variable_2="I_V_Minus" />
</connection>
<component name="membraneV_delta">
<variable name="IStim" public_interface="in" units="uA_per_mm2"/>
<variable name="IMinusExternal" public_interface="in" units="uA_per_mm2"/>
<variable name="INetMinus" units="uA_per_mm2" public_interface="out" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply><eq/>
<ci>INetMinus</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>IStim</ci>
<ci>IMinusExternal</ci>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="membraneV_delta"/>
<map_variables variable_1="I_V_MinusExternal" variable_2="IMinusExternal" />
</connection>
<connection>
<map_components component_1="membraneV_delta" component_2="ICaL_to_Cai"/>
<map_variables variable_1="INetMinus" variable_2="I_V_MinusExternal" />
</connection>
<connection>
<map_components component_1="membraneV_delta" component_2="StimCurrent_SinglePulse"/>
<map_variables variable_1="IStim" variable_2="IStim"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Myosin_ATPASE.cellml">
<component name="Myosin_ATPASE" component_ref="Myosin_ATPASE"/>
<units name="M" units_ref="M" />
<units name="per_s" units_ref="per_s" />
<units name="M_per_s" units_ref="M_per_s" />
</import>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="Myosin_ATPASE"/>
<map_variables variable_1="time" variable_2="time" />
<map_variables variable_1="ATP_init" variable_2="ATP_init" />
<map_variables variable_1="ADP_init" variable_2="ADP_init" />
<map_variables variable_1="H_init" variable_2="H_init" />
<map_variables variable_1="Pi_init" variable_2="Pi_init" />
<map_variables variable_1="Mg_init" variable_2="Mg_init" />
<map_variables variable_1="K_init" variable_2="K_init" />
<map_variables variable_1="BX" variable_2="BX" />
<map_variables variable_1="K_BX" variable_2="K_BX" />
<map_variables variable_1="ATPASE_p1" variable_2="ATPASE_p1" />
<map_variables variable_1="Env" variable_2="Env" />
<map_variables variable_1="Kh1" variable_2="Kh1" />
<map_variables variable_1="Km1" variable_2="Km1" />
<map_variables variable_1="Kk1" variable_2="Kk1" />
<map_variables variable_1="Kh2" variable_2="Kh2" />
<map_variables variable_1="Km2" variable_2="Km2" />
<map_variables variable_1="Kk2" variable_2="Kk2" />
<map_variables variable_1="Kh3" variable_2="Kh3" />
<map_variables variable_1="Km3" variable_2="Km3" />
<map_variables variable_1="Kk3" variable_2="Kk3" />
<map_variables variable_1="DGro_ATPASE" variable_2="DGro_ATPASE"/>
<map_variables variable_1="J_ATP_External" variable_2="J_ATP_External" />
<map_variables variable_1="J_ADP_External" variable_2="J_ADP_External" />
<map_variables variable_1="J_H_External" variable_2="J_H_External" />
<map_variables variable_1="J_Pi_External" variable_2="J_Pi_External" />
<map_variables variable_1="J_Mg_External" variable_2="J_Mg_External" />
<map_variables variable_1="J_K_External" variable_2="J_K_External" />
<map_variables variable_1="ATP" variable_2="ATP" />
<map_variables variable_1="ADP" variable_2="ADP" />
<map_variables variable_1="Pi" variable_2="Pi" />
<map_variables variable_1="H" variable_2="H" />
<map_variables variable_1="Mg" variable_2="Mg" />
<map_variables variable_1="K" variable_2="K" />
<map_variables variable_1="J_H" variable_2="J_H" />
<map_variables variable_1="J_ATP" variable_2="J_ATP" />
<map_variables variable_1="J_ADP" variable_2="J_ADP" />
<map_variables variable_1="J_Pi" variable_2="J_Pi" />
<map_variables variable_1="J_Mg" variable_2="J_Mg" />
<map_variables variable_1="J_K" variable_2="J_K" />
</connection>
<connection>
<map_components component_1="Myosin_ATPASE" component_2="ICaL_to_Cai"/>
<map_variables variable_1="ATP" variable_2="ATP_i" />
<map_variables variable_1="H" variable_2="H_i" />
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Calmodulin_Activation.cellml">
<component name="Calmodulin_Activation" component_ref="Calmodulin_Activation"/>
<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>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="Calmodulin_Activation"/>
<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="kon" variable_2="kon"/>
<map_variables variable_1="koff" variable_2="koff"/>
<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"/>
<map_variables variable_1="CaM" variable_2="CaM" />
<map_variables variable_1="J_CaM" variable_2="J_CaM" />
<map_variables variable_1="CaM_star" variable_2="CaM_star" />
<map_variables variable_1="J_CaM_star" variable_2="J_CaM_star" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="Calmodulin_Activation" component_2="ICaL_to_Cai"/>
<map_variables variable_1="Ca" variable_2="Cai" />
</connection>
<component name="Cai_delta">
<variable name="JMinusCaMActivation" public_interface="in" units="mM_per_s" />
<variable name="JNet" units="mM_per_s" public_interface="out" />
<variable name="JExternal" units="mM_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<minus/>
<ci>JExternal</ci>
<ci>JMinusCaMActivation</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="Cai_delta"/>
<map_variables variable_1="J_Cai_External" variable_2="JExternal" />
</connection>
<connection>
<map_components component_1="Cai_delta" component_2="ICaL_to_Cai"/>
<map_variables variable_1="JNet" variable_2="J_Cai_External" />
</connection>
<connection>
<map_components component_1="CaMActivation_Ca_J_Scaling" component_2="Cai_delta"/>
<map_variables variable_1="J_scaled" variable_2="JMinusCaMActivation"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_FluxScaling_uM.cellml">
<component name="CaMActivation_Ca_J_Scaling" component_ref="Template_FluxScaling_uM"/>
</import>
<connection>
<map_components component_1="Calmodulin_Activation" component_2="CaMActivation_Ca_J_Scaling"/>
<map_variables variable_1="J_CaM_star" variable_2="J_raw"/>
</connection>
<connection>
<map_components component_1="CaMActivation_Ca_J_Scaling" component_2="ACoreDomainsExample"/>
<map_variables variable_1="scaleFactor" variable_2="CaMActivation_Ca_J_ScaleFactor"/>
</connection>
<import xlink:href="CaN_to_DNAReady_NFAT.cellml">
<units name="nM" units_ref="nM" />
<units name="nM_per_s" units_ref="nM_per_s" />
<units name="per_nM_per_s" units_ref="per_nM_per_s" />
<component name="CaN_to_DNAReady_NFAT" component_ref="CaN_to_DNAReady_NFAT"/>
</import>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="CaN_to_DNAReady_NFAT"/>
<map_variables variable_1="time" variable_2="time" />
<map_variables variable_1="Ccn" variable_2="Ccn" />
<map_variables variable_1="Ntot" variable_2="Ntot" />
<map_variables variable_1="k_f1" variable_2="k_f1" />
<map_variables variable_1="k_r1" variable_2="k_r1" />
<map_variables variable_1="k_f2" variable_2="k_f2" />
<map_variables variable_1="k_f3" variable_2="k_f3" />
<map_variables variable_1="k_r3" variable_2="k_r3" />
<map_variables variable_1="k_f4" variable_2="k_f4" />
<map_variables variable_1="NFATp_c_init" variable_2="NFATp_c_init" />
<map_variables variable_1="NFATN_c_init" variable_2="NFATN_c_init" />
<map_variables variable_1="NFATN_n_init" variable_2="NFATN_n_init" />
<map_variables variable_1="NFATp_n_init" variable_2="NFATp_n_init" />
<map_variables variable_1="J_NFATp_c_External" variable_2="J_NFATp_c_External" />
<map_variables variable_1="J_NFATN_c_External" variable_2="J_NFATN_c_External" />
<map_variables variable_1="J_NFATN_n_External" variable_2="J_NFATN_n_External" />
<map_variables variable_1="J_NFATp_n_External" variable_2="J_NFATp_n_External" />
<map_variables variable_1="K_mN" variable_2="K_mN"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="K_dN" variable_2="K_dN"/>
<map_variables variable_1="N_active_ratio" variable_2="N_active_ratio"/>
<map_variables variable_1="NFATp_c" variable_2="NFATp_c" />
<map_variables variable_1="NFATN_c" variable_2="NFATN_c" />
<map_variables variable_1="NFATN_n" variable_2="NFATN_n" />
<map_variables variable_1="NFATp_n" variable_2="NFATp_n" />
<map_variables variable_1="J_NFATp_c" variable_2="J_NFATp_c" />
<map_variables variable_1="J_NFATN_c" variable_2="J_NFATN_c" />
<map_variables variable_1="J_NFATN_n" variable_2="J_NFATN_n" />
<map_variables variable_1="J_NFATp_n" variable_2="J_NFATp_n" />
<map_variables variable_1="CaM_total" variable_2="M"/>
</connection>
<connection>
<map_components component_1="CaN_to_DNAReady_NFAT" component_2="ICaL_to_Cai"/>
<map_variables variable_1="Ca" variable_2="Cai"/>
</connection>
<import xlink:href="ExampleDevice.cellml">
<units name="PoPs" units_ref="PoPs"/>
<units name="RiPs" units_ref="RiPs"/>
<units name="femtoliter" units_ref="femtoliter"/>
<component name="ExampleDevice" component_ref="ExampleDevice"/>
</import>
<connection>
<map_components component_1="ACoreDomainsExample" component_2="ExampleDevice"/>
<map_variables variable_1="time" variable_2="time" />
<map_variables variable_1="Promoter_GFP_k" variable_2="k"/>
<map_variables variable_1="Promoter_GFP_n" variable_2="n"/>
<map_variables variable_1="Promoter_GFP_Km" variable_2="Km"/>
<map_variables variable_1="transcriptionalVolume_init" variable_2="transcriptionalVolume_init"/>
<map_variables variable_1="translationalVolume_init" variable_2="translationalVolume_init"/>
<map_variables variable_1="RNA_n_init" variable_2="RNA_n_init"/>
<map_variables variable_1="J_RNA_n_External" variable_2="J_RNA_n_External"/>
<map_variables variable_1="RNA_c_init" variable_2="RNA_c_init"/>
<map_variables variable_1="J_RNA_c_External" variable_2="J_RNA_c_External"/>
<map_variables variable_1="GFP_init" variable_2="GFP_init"/>
<map_variables variable_1="J_GFP_External" variable_2="J_GFP_External"/>
<map_variables variable_1="RBS_k" variable_2="RBS_k"/>
<map_variables variable_1="RNA_kDecay" variable_2="RNA_kDecay"/>
<map_variables variable_1="RNA_Transport_k" variable_2="RNA_Transport_k"/>
<map_variables variable_1="GFP_kDecay" variable_2="GFP_kDecay"/>
<map_variables variable_1="avogadrosConstant" variable_2="avogadrosConstant"/>
<map_variables variable_1="J_RNA_n" variable_2="J_RNA_n" />
<map_variables variable_1="RNA_n" variable_2="RNA_n" />
<map_variables variable_1="J_RNA_c" variable_2="J_RNA_c" />
<map_variables variable_1="RNA_c" variable_2="RNA_c" />
<map_variables variable_1="transcriptionalVolume" variable_2="transcriptionalVolume"/>
<map_variables variable_1="translationalVolume" variable_2="translationalVolume"/>
<map_variables variable_1="J_GFP" variable_2="J_GFP" />
<map_variables variable_1="GFP" variable_2="GFP" />
</connection>
<connection>
<map_components component_1="CaN_to_DNAReady_NFAT" component_2="ExampleDevice"/>
<map_variables variable_1="NFATN_n" variable_2="transcriptionFactor" />
</connection>
</model>
