- Author:
- Mona Zhu <devnull@localhost>
- Date:
- 2011-01-06 15:31:49+13:00
- Desc:
- Adding 1.1 models (first time)
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/leloup_goldbeter_1998/rawfile/beb46ba0d855ed2abd72a2ce0ce210ff7a36f752/leloup_1998b_1.1model.cellml
<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.1#" cmeta:id="leloup_1998b_1.1model" name="leloup_1998b_1.1model"><group><relationship_ref relationship="encapsulation"/><component_ref component="cytosol"><component_ref component="PER"><component_ref component="P0"/><component_ref component="P1"/><component_ref component="P2"/></component_ref><component_ref component="TIM"><component_ref component="T0"/><component_ref component="T1"/><component_ref component="T2"/><component_ref component="LD_cycle"/></component_ref></component_ref></group>
<units name="hour">
<unit multiplier="3600" units="second"/>
</units>
<units name="per_hour">
<unit exponent="-1" units="hour"/>
</units>
<units name="per_litre">
<unit exponent="-1" units="litre"/>
</units>
<units name="nanomolar">
<unit prefix="nano" units="mole"/>
<unit units="per_litre"/>
</units>
<units name="nanomolar_hour">
<unit units="nanomolar"/>
<unit units="per_hour"/>
</units>
<units name="per_nanomolar_hour">
<unit exponent="-1" units="nanomolar"/>
<unit units="per_hour"/>
</units><component name="environment">
<variable id="environment_time" name="time" public_interface="out" units="hour"/>
</component><component id="nucleus" name="nucleus">
<variable name="time" private_interface="out" public_interface="in" units="hour"/>
<variable initial_value="0.8" name="v_sP" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="0.8" name="v_mP" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="1" name="K_IP" private_interface="out" units="nanomolar"/>
<variable initial_value="0.2" name="K_mP" private_interface="out" units="nanomolar"/>
<variable initial_value="1" name="v_sT" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="0.7" name="v_mT" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="1" name="K_IT" private_interface="out" units="nanomolar"/>
<variable initial_value="0.2" name="K_mT" private_interface="out" units="nanomolar"/>
<variable name="k_d" private_interface="out" public_interface="in" units="per_hour"/>
<variable initial_value="4" name="n" private_interface="out" units="dimensionless"/>
<variable name="k_1" private_interface="out" public_interface="in" units="per_hour"/>
<variable name="k_2" private_interface="out" public_interface="in" units="per_hour"/>
<variable initial_value="0.01" name="k_dN" private_interface="out" units="per_hour"/>
<variable name="C" private_interface="out" public_interface="in" units="nanomolar"/>
<variable id="M_P" name="M_P" private_interface="in" public_interface="out" units="nanomolar"/>
<variable id="M_T" name="M_T" private_interface="in" public_interface="out" units="nanomolar"/>
<variable id="C_N" initial_value="1.203" name="C_N" private_interface="out" public_interface="out" units="nanomolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML"><apply><eq/><apply><diff/><bvar><ci>time</ci></bvar><ci>C_N</ci></apply><apply><minus/><apply><minus/><apply><times/><ci>k_1</ci><ci>C</ci></apply><apply><times/><ci>k_2</ci><ci>C_N</ci></apply></apply><apply><times/><ci>k_dN</ci><ci>C_N</ci></apply></apply></apply></math>
<variable initial_value="0.09107" name="M_Pinit" private_interface="out" units="nanomolar"/><variable initial_value="1.427" name="M_Tinit" private_interface="out" units="nanomolar"/></component><component id="cytosol" name="cytosol">
<variable name="time" private_interface="out" public_interface="in" units="hour"/>
<variable initial_value="1.2" name="k_1" public_interface="out" units="per_hour"/>
<variable initial_value="0.2" name="k_2" public_interface="out" units="per_hour"/>
<variable initial_value="1.2" name="k_3" private_interface="out" units="per_nanomolar_hour"/>
<variable initial_value="0.6" name="k_4" private_interface="out" units="per_hour"/>
<variable initial_value="0.01" name="k_d" private_interface="out" public_interface="out" units="per_hour"/>
<variable initial_value="0.01" name="k_dC" units="per_hour"/>
<variable name="P_0" private_interface="in" public_interface="out" units="nanomolar"/>
<variable name="P_1" private_interface="in" public_interface="out" units="nanomolar"/>
<variable name="P_2" private_interface="in" public_interface="out" units="nanomolar"/>
<variable name="T_0" private_interface="in" public_interface="out" units="nanomolar"/>
<variable name="T_1" private_interface="in" public_interface="out" units="nanomolar"/>
<variable name="T_2" private_interface="in" public_interface="out" units="nanomolar"/>
<variable name="M_P" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="M_T" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C_N" public_interface="in" units="nanomolar"/>
<variable id="C" initial_value="0.1790" name="C" private_interface="out" public_interface="out" units="nanomolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>C</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_3</ci>
<ci>P_2</ci>
<ci>T_2</ci>
</apply>
<apply>
<times/>
<ci>k_4</ci>
<ci>C</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_1</ci>
<ci>C</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_2</ci>
<ci>C_N</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_dC</ci>
<ci>C</ci>
</apply>
</apply>
</apply>
</math>
</component><component id="PER" name="PER">
<variable name="time" private_interface="out" public_interface="in" units="hour"/>
<variable initial_value="8" name="V_1P" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="1" name="V_2P" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="8" name="V_3P" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="1" name="V_4P" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="2" name="K_1P" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="K_2P" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="K_3P" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="K_4P" private_interface="out" units="nanomolar"/>
<variable initial_value="0.2" name="K_dP" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="v_dP" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="0.9" name="k_sP" private_interface="out" units="per_hour"/>
<variable name="k_d" private_interface="out" public_interface="in" units="per_hour"/>
<variable name="k_3" private_interface="out" public_interface="in" units="per_nanomolar_hour"/>
<variable name="k_4" private_interface="out" public_interface="in" units="per_hour"/>
<variable name="M_P" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="T_2" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C" private_interface="out" public_interface="in" units="nanomolar"/>
<variable id="P_0" name="P_0" private_interface="in" public_interface="out" units="nanomolar"/>
<variable id="P_1" name="P_1" private_interface="in" public_interface="out" units="nanomolar"/>
<variable id="P_2" name="P_2" private_interface="in" public_interface="out" units="nanomolar"/>
<variable initial_value="0.02324" name="P_0init" private_interface="out" units="nanomolar"/><variable initial_value="0.02210" name="P_1init" private_interface="out" units="nanomolar"/><variable initial_value="0.01251" name="P_2init" private_interface="out" units="nanomolar"/></component><component id="TIM" name="TIM">
<variable name="time" private_interface="out" public_interface="in" units="hour"/>
<variable initial_value="8" name="V_1T" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="1" name="V_2T" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="8" name="V_3T" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="1" name="V_4T" private_interface="out" units="nanomolar_hour"/>
<variable initial_value="2" name="K_1T" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="K_2T" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="K_3T" private_interface="out" units="nanomolar"/>
<variable initial_value="2" name="K_4T" private_interface="out" units="nanomolar"/>
<variable initial_value="0.2" name="K_dT" private_interface="out" units="nanomolar"/>
<variable name="v_dT" private_interface="in" units="nanomolar_hour"/>
<variable initial_value="0.9" name="k_sT" private_interface="out" units="per_hour"/>
<variable name="k_d" private_interface="out" public_interface="in" units="per_hour"/>
<variable name="k_3" private_interface="out" public_interface="in" units="per_nanomolar_hour"/>
<variable name="k_4" private_interface="out" public_interface="in" units="per_hour"/>
<variable name="M_T" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="P_2" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C" private_interface="out" public_interface="in" units="nanomolar"/>
<variable id="T_0" name="T_0" private_interface="in" public_interface="out" units="nanomolar"/>
<variable id="T_1" name="T_1" private_interface="in" public_interface="out" units="nanomolar"/>
<variable id="T_2" name="T_2" private_interface="in" public_interface="out" units="nanomolar"/>
<variable initial_value="0.5420" name="T_0init" private_interface="out" units="nanomolar"/><variable initial_value="0.8000" name="T_1init" private_interface="out" units="nanomolar"/><variable initial_value="4.733" name="T_2init" private_interface="out" units="nanomolar"/></component><component id="PER_total" name="PER_total">
<variable name="P_0" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="P_1" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="P_2" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C_N" private_interface="out" public_interface="in" units="nanomolar"/>
<variable id="P_t" name="P_t" private_interface="in" units="nanomolar"/>
</component><component id="TIM_total" name="TIM_total">
<variable name="T_0" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="T_1" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="T_2" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C" private_interface="out" public_interface="in" units="nanomolar"/>
<variable name="C_N" private_interface="out" public_interface="in" units="nanomolar"/>
<variable id="T_t" name="T_t" private_interface="in" units="nanomolar"/>
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variable_2="V_3T"/><map_variables variable_1="V_4" variable_2="V_4T"/><map_variables variable_1="K_1" variable_2="K_1T"/><map_variables variable_1="K_2" variable_2="K_2T"/><map_variables variable_1="K_3" variable_2="K_3T"/><map_variables variable_1="K_4" variable_2="K_4T"/><map_variables variable_1="k_d" variable_2="k_d"/><map_variables variable_1="Y_1init" variable_2="T_1init"/></connection><connection><map_components component_1="T2" component_2="TIM"/><map_variables variable_1="Y_2" variable_2="T_2"/><map_variables variable_1="time" variable_2="time"/><map_variables variable_1="V_3" variable_2="V_3T"/><map_variables variable_1="V_4" variable_2="V_4T"/><map_variables variable_1="K_3" variable_2="K_3T"/><map_variables variable_1="K_4" variable_2="K_4T"/><map_variables variable_1="K_d" variable_2="K_dT"/><map_variables variable_1="k_3" variable_2="k_3"/><map_variables variable_1="k_4" variable_2="k_4"/><map_variables variable_1="k_d" variable_2="k_d"/><map_variables variable_1="Z_2" variable_2="P_2"/><map_variables variable_1="C" variable_2="C"/><map_variables variable_1="v_d" variable_2="v_dT"/><map_variables variable_1="Y_2init" variable_2="T_2init"/></connection><connection><map_components component_1="PERtotal" component_2="PER_total"/><map_variables variable_1="Y_t" variable_2="P_t"/><map_variables variable_1="Y_0" variable_2="P_0"/><map_variables variable_1="Y_1" variable_2="P_1"/><map_variables variable_1="Y_2" variable_2="P_2"/><map_variables variable_1="C" variable_2="C"/><map_variables variable_1="C_N" variable_2="C_N"/></connection><connection><map_components component_1="TIMtotal" component_2="TIM_total"/><map_variables variable_1="Y_t" variable_2="T_t"/><map_variables variable_1="Y_0" variable_2="T_0"/><map_variables variable_1="Y_1" variable_2="T_1"/><map_variables variable_1="Y_2" variable_2="T_2"/><map_variables variable_1="C" variable_2="C"/><map_variables variable_1="C_N" variable_2="C_N"/></connection><group><relationship_ref relationship="encapsulation"/><component_ref component="PER_total"><component_ref component="PERtotal"/></component_ref></group><group><relationship_ref relationship="encapsulation"/><component_ref component="TIM_total"><component_ref component="TIMtotal"/></component_ref></group><connection><map_components component_1="P0" component_2="P1"/><map_variables variable_1="Y_0" variable_2="Y_0"/><map_variables variable_1="Y_1" variable_2="Y_1"/></connection><connection><map_components component_1="P1" component_2="P2"/><map_variables variable_1="Y_1" variable_2="Y_1"/><map_variables variable_1="Y_2" variable_2="Y_2"/></connection><connection><map_components component_1="T0" component_2="T1"/><map_variables variable_1="Y_0" variable_2="Y_0"/><map_variables variable_1="Y_1" variable_2="Y_1"/></connection><connection><map_components component_1="T1" component_2="T2"/><map_variables variable_1="Y_1" variable_2="Y_1"/><map_variables variable_1="Y_2" variable_2="Y_2"/></connection><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:nodeID="n1"><endingValue xmlns="http://www.cellml.org/metadata/simulation/1.1#" xml:lang="en">72</endingValue></rdf:Description><rdf:Description rdf:nodeID="n2"><rdf:first><rdf:Description rdf:nodeID="n1"/></rdf:first><rdf:rest><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/></rdf:rest></rdf:Description><rdf:Description rdf:about="#mO8ltXqJk40"><simulation xmlns="http://www.cellml.org/metadata/simulation/1.1#"><rdf:Description rdf:nodeID="n3"/></simulation></rdf:Description><rdf:Description rdf:nodeID="n3"><boundIntervals xmlns="http://www.cellml.org/metadata/simulation/1.1#"><rdf:Description rdf:nodeID="n2"/></boundIntervals></rdf:Description></rdf:RDF><component cmeta:id="LD_cycle" name="LD_cycle">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#LD_cycle">This component creates the v_dT oscillation to account for the light-induced TIM degration in the 12:12 LD cycle</rdf:Description>
<rdf:Description rdf:about="#v_dT">maximum rate enzyme degration of the fully phosphorylated TIM (affected by exposure to light)</rdf:Description>
</rdf:RDF>
<variable name="time" public_interface="in" units="hour"/>
<variable initial_value="3.141592653589793" name="PI" units="dimensionless"/>
<variable initial_value="2" name="v_dT_dark" units="nanomolar_hour"/>
<variable initial_value="4" name="v_dT_light" units="nanomolar_hour"/>
<variable cmeta:id="v_dT" name="v_dT" public_interface="out" units="nanomolar_hour"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v_dT</ci>
<piecewise>
<piece>
<ci>v_dT_dark</ci>
<apply>
<leq/>
<apply>
<sin/>
<apply>
<divide/>
<apply>
<times/>
<ci>PI</ci>
<ci>time</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="hour">12</cn>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">0</cn>
</apply>
</piece>
<otherwise>
<ci>v_dT_light</ci>
</otherwise>
</piecewise>
</apply>
</math>
</component><connection>
<map_components component_1="TIM" component_2="LD_cycle"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="v_dT" variable_2="v_dT"/>
</connection><connection><map_components component_1="T2" component_2="LD_cycle"/><map_variables variable_1="v_d" variable_2="v_dT"/></connection></model>
