- 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.cellml.org/workspace/2c5/rawfile/cce6374c21a60771321701b2f88857175ca5c31e/NFAT_Cycling.cellml
<?xml version="1.0" encoding="utf-8"?>
<model xmlns:xlink="http://www.w3.org/1999/xlink" name="NFAT_Cycling" cmeta:id="NFAT_Cycling"
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="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"/>
</import>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Time.cellml">
<component name="Time" component_ref="Time"/>
</import>
<group>
<relationship_ref relationship="encapsulation" />
<component_ref component="NFAT_Cycling">
<component_ref component="NFATp_c" />
<component_ref component="NFATp_c_delta" />
<component_ref component="NFATN_c" />
<component_ref component="NFATN_c_delta" />
<component_ref component="NFATN_n" />
<component_ref component="NFATN_n_delta" />
<component_ref component="NFATp_n" />
<component_ref component="NFATp_n_delta" />
<component_ref component="R1" />
<component_ref component="R3" />
<component_ref component="R2" />
<component_ref component="R4" />
</component_ref>
</group>
<component name="NFAT_Cycling_Parameters">
<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_f1" units="per_nM_per_s" initial_value="7.68934e-6" public_interface="out"/>
<variable name="k_r1" units="per_s" initial_value="0.019256" public_interface="out"/>
<variable name="k_f2" units="per_s" initial_value="0.00144192" public_interface="out"/>
<variable name="k_f3" units="per_s" initial_value="0.000361944" public_interface="out"/>
<variable name="k_r3" units="per_nM_per_s" initial_value="4.70813e-5" public_interface="out"/>
<variable name="k_f4" units="per_s" initial_value="0.000444695" public_interface="out"/>
<variable name="NFATp_c_init" units="nM" initial_value="1.0" public_interface="out"/>
<variable name="NFATN_c_init" units="nM" initial_value="0" public_interface="out"/>
<variable name="NFATN_n_init" units="nM" initial_value="0" public_interface="out"/>
<variable name="NFATp_n_init" units="nM" initial_value="0" 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"/>
</component>
<component name="NFAT_Cycling">
<variable name="time" units="second" public_interface="in" private_interface="out"/>
<variable name="Ntot" units="nM" public_interface="in" private_interface="out"/>
<variable name="act_N" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Ccn" units="dimensionless" 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"/>
<variable name="k_f2" units="per_s" public_interface="in" private_interface="out"/>
<variable name="k_f3" units="per_s" public_interface="in" />
<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="N_active" units="nM" public_interface="out" private_interface="out"/>
<variable name="inact_N" units="dimensionless" />
<variable name="k_r1_scaled" units="per_s" private_interface="out"/>
<variable name="k_f3_scaled" units="per_s" private_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"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>N_active</ci>
<apply>
<times/>
<ci>Ntot</ci>
<ci>act_N</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>inact_N</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>act_N</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_r1_scaled</ci>
<apply>
<times/>
<ci>k_r1</ci>
<ci>inact_N</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_f3_scaled</ci>
<apply>
<times/>
<ci>k_f3</ci>
<ci>inact_N</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="Time" component_2="NFAT_Cycling"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="NFAT_Cycling_Parameters" component_2="NFAT_Cycling"/>
<map_variables variable_1="act_N" variable_2="act_N"/>
<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="Ccn" variable_2="Ccn"/>
<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"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
<units name="per_s" units_ref="per_s"/>
<component name="NFATp_c" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="NFATp_c" component_2="NFAT_Cycling"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentrationInitialValue" variable_2="NFATp_c_init"/>
<map_variables variable_1="concentration" variable_2="NFATp_c"/>
</connection>
<connection>
<map_components component_1="NFATp_c" component_2="NFATp_c_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="NFAT_Cycling" component_2="NFATp_c_delta"/>
<map_variables variable_1="Ccn" variable_2="Ccn"/>
<map_variables variable_1="J_NFATp_c_External" variable_2="JPlusExternal"/>
<map_variables variable_1="J_NFATp_c" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="R4" component_2="NFATp_c_delta"/>
<map_variables variable_1="J" variable_2="JPlusR4"/>
</connection>
<connection>
<map_components component_1="R1" component_2="NFATp_c_delta"/>
<map_variables variable_1="J" variable_2="JMinusR1"/>
</connection>
<component name="NFATp_c_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusR4" units="nM_per_s" public_interface="in" />
<variable name="JMinusR1" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<variable name="Ccn" units="dimensionless" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<apply>
<divide/>
<ci>JPlusR4</ci>
<ci>Ccn</ci>
</apply>
</apply>
<ci>JMinusR1</ci>
</apply>
</apply>
</math>
</component>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
<component name="NFATN_c" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="NFATN_c" component_2="NFAT_Cycling"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentrationInitialValue" variable_2="NFATN_c_init"/>
<map_variables variable_1="concentration" variable_2="NFATN_c"/>
</connection>
<connection>
<map_components component_1="NFATN_c_delta" component_2="NFAT_Cycling"/>
<map_variables variable_1="JPlusExternal" variable_2="J_NFATN_c_External"/>
<map_variables variable_1="JNet" variable_2="J_NFATN_c"/>
</connection>
<connection>
<map_components component_1="NFATN_c" component_2="NFATN_c_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="R2" component_2="NFATN_c_delta"/>
<map_variables variable_1="J" variable_2="JMinusR2"/>
</connection>
<connection>
<map_components component_1="R1" component_2="NFATN_c_delta"/>
<map_variables variable_1="J" variable_2="JPlusR1"/>
</connection>
<component name="NFATN_c_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusR1" units="nM_per_s" public_interface="in" />
<variable name="JMinusR2" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<apply>
<minus/>
<ci>JPlusR1</ci>
<ci>JMinusR2</ci>
</apply>
</apply>
</apply>
</math>
</component>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
<component name="NFATN_n" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="NFATN_n" component_2="NFAT_Cycling"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentrationInitialValue" variable_2="NFATN_n_init"/>
<map_variables variable_1="concentration" variable_2="NFATN_n"/>
</connection>
<connection>
<map_components component_1="NFATN_n" component_2="NFATN_n_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="NFATN_n_delta" component_2="NFAT_Cycling"/>
<map_variables variable_1="Ccn" variable_2="Ccn"/>
<map_variables variable_1="JPlusExternal" variable_2="J_NFATN_n_External"/>
<map_variables variable_1="JNet" variable_2="J_NFATN_n"/>
</connection>
<connection>
<map_components component_1="NFATN_n_delta" component_2="R2"/>
<map_variables variable_1="JPlusR2" variable_2="J"/>
</connection>
<connection>
<map_components component_1="NFATN_n_delta" component_2="R3"/>
<map_variables variable_1="JMinusR3" variable_2="J"/>
</connection>
<component name="NFATN_n_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusR2" units="nM_per_s" public_interface="in" />
<variable name="JMinusR3" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<variable name="Ccn" units="dimensionless" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<apply>
<times/>
<ci>JPlusR2</ci>
<ci>Ccn</ci>
</apply>
</apply>
<ci>JMinusR3</ci>
</apply>
</apply>
</math>
</component>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_Species_uM.cellml">
<component name="NFATp_n" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="NFATp_n" component_2="NFAT_Cycling"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentrationInitialValue" variable_2="NFATp_n_init"/>
<map_variables variable_1="concentration" variable_2="NFATp_n"/>
</connection>
<connection>
<map_components component_1="NFATp_n_delta" component_2="NFAT_Cycling"/>
<map_variables variable_1="JPlusExternal" variable_2="J_NFATp_n_External"/>
<map_variables variable_1="JNet" variable_2="J_NFATp_n"/>
</connection>
<connection>
<map_components component_1="NFATp_n" component_2="NFATp_n_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="NFATp_n_delta" component_2="R4"/>
<map_variables variable_1="JMinusR4" variable_2="J"/>
</connection>
<connection>
<map_components component_1="NFATp_n_delta" component_2="R3"/>
<map_variables variable_1="JPlusR3" variable_2="J"/>
</connection>
<component name="NFATp_n_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusR3" units="nM_per_s" public_interface="in" />
<variable name="JMinusR4" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<apply>
<minus/>
<ci>JPlusR3</ci>
<ci>JMinusR4</ci>
</apply>
</apply>
</apply>
</math>
</component>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR2P1_uM.cellml">
<component name="R1" component_ref="Template_RateEqR2P1_uM"/>
</import>
<connection>
<map_components component_1="R1" component_2="NFAT_Cycling"/>
<map_variables variable_1="kf" variable_2="k_f1"/>
<map_variables variable_1="kr" variable_2="k_r1_scaled"/>
<map_variables variable_1="B" variable_2="N_active"/>
</connection>
<connection>
<map_components component_1="R1" component_2="NFATp_c"/>
<map_variables variable_1="A" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="R1" component_2="NFATN_c"/>
<map_variables variable_1="C" variable_2="concentration"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1P2_uM.cellml">
<component name="R3" component_ref="Template_RateEqR1P2_uM"/>
</import>
<connection>
<map_components component_1="R3" component_2="NFAT_Cycling"/>
<map_variables variable_1="kr" variable_2="k_r3"/>
<map_variables variable_1="kf" variable_2="k_f3_scaled"/>
<map_variables variable_1="B" variable_2="N_active"/>
</connection>
<connection>
<map_components component_1="R3" component_2="NFATN_n"/>
<map_variables variable_1="A" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="R3" component_2="NFATp_n"/>
<map_variables variable_1="C" variable_2="concentration"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1_uM.cellml">
<component name="R2" component_ref="Template_RateEqR1_uM"/>
</import>
<connection>
<map_components component_1="R2" component_2="NFAT_Cycling"/>
<map_variables variable_1="k" variable_2="k_f2"/>
</connection>
<connection>
<map_components component_1="R2" component_2="NFATN_c"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<import xmlns="http://www.cellml.org/cellml/1.1#" xlink:href="Principled_Base/Template_RateEqR1_uM.cellml">
<component name="R4" component_ref="Template_RateEqR1_uM"/>
</import>
<connection>
<map_components component_1="R4" component_2="NFAT_Cycling"/>
<map_variables variable_1="k" variable_2="k_f4"/>
</connection>
<connection>
<map_components component_1="R4" component_2="NFATp_n"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
</model>
