def model sinIsinR as
   def unit per_s from
      unit second {expo: -1};
   enddef;

   def unit M from
      unit mole;
      unit liter {expo: -1};
   enddef;

   def unit nM from
      unit M {pref: nano};
   enddef;

   def unit per_nM from
      unit nM {expo: -1};
   enddef;

   def unit nM_per_s from
      unit nM;
      unit per_s;
   enddef;

   def comp temporalExistence as
      var time: second {pub: out};
   enddef;

   def comp P1_Promoter_Activity as
      var alpha_1: dimensionless {pub: out};
      var R_4: dimensionless {pub: in};
      var RNAP: dimensionless {init: 30};
      var S2: dimensionless {init: 5};
      var K2: dimensionless;
      var K3: dimensionless;
      var K4: dimensionless;
      var K5: dimensionless;
      var K6: dimensionless;
      var K7: dimensionless;
      var K8: dimensionless;
      var RT: dimensionless {init: 1.62};
      var G2: dimensionless {init: -10.5};
      var G3: dimensionless {init: -12.5};
      var G4: dimensionless {init: -9};
      var G5: dimensionless {init: -21.5};
      var G6: dimensionless {init: -21.5};
      var G7: dimensionless {init: -22.5};
      var G8: dimensionless {init: -33.5};

      K2 = exp(-G2/RT)*1e-9{dimensionless};
      K3 = exp(-G3/RT)*1e-9{dimensionless};
      K4 = exp(-G4/RT)*1e-9{dimensionless};
      K5 = exp(-G5/RT)*1e-9{dimensionless};
      K6 = exp(-G6/RT)*1e-9{dimensionless};
      K7 = exp(-G7/RT)*1e-9{dimensionless};
      K8 = exp(-G8/RT)*1e-9{dimensionless};
      alpha_1 = K6*RNAP*S2/(1{dimensionless}+K2*RNAP+K3*R_4+K4*S2+K5*S2*R_4+K6*S2*RNAP+K7*RNAP*R_4+K8*S2*RNAP*R_4);
   enddef;

   def comp P1_Transcription as
      var time: second {pub: in};
      var k_1: per_s {init: 0.15};
      var alpha_1: dimensionless {pub: in};
      var gamma_1: per_s {init: 0.005};
      var m_1: dimensionless {init: 0, pub: out};

      ode(m_1, time) = k_1*alpha_1-gamma_1*m_1;
   enddef;

   def comp P3_Transcription as
      var time: second {pub: in};
      var k_3: per_s {init: 0.02};
      var gamma_3: per_s {init: 0.005};
      var m_3: dimensionless {init: 0, pub: out};

      ode(m_3, time) = k_3-gamma_3*m_3;
   enddef;

   def comp SinI_Interface as
      var JTotal: per_s {pub: out};
      var m_1: dimensionless {pub: in};
      var A_I: per_s {init: 0.8};
      var JDegradation: per_s {pub: in};
      var J_IR_Formation: per_s {pub: in};

      JTotal = A_I*m_1-JDegradation-J_IR_Formation;
   enddef;

   def comp SinI_Degradation as
      var gamma_I: per_s {init: 0.02};
      var I: dimensionless {pub: in};
      var JDegradation: per_s {pub: out};

      JDegradation = gamma_I*I;
   enddef;

   def comp SinI as
      var time: second {pub: in};
      var JTotal: per_s {pub: in};
      var I: dimensionless {init: 0, pub: out};

      ode(I, time) = JTotal;
   enddef;

   def comp IR_Formation as
      var J_IR_Formation: per_s {pub: out};
      var k_on_I: per_s {init: 0.083};
      var I: dimensionless {pub: in};
      var R: dimensionless {pub: in};
      var k_off_I: per_s {init: 0.5};
      var IR: dimensionless {pub: in};

      J_IR_Formation = k_on_I*I*R-k_off_I*IR;
   enddef;

   def comp IR_Interface as
      var JTotal: per_s {pub: out};
      var JDegradation: per_s {pub: in};
      var J_IR_Formation: per_s {pub: in};

      JTotal = J_IR_Formation-JDegradation;
   enddef;

   def comp IR as
      var time: second {pub: in};
      var JTotal: per_s {pub: in};
      var IR: dimensionless {init: 0, pub: out};

      ode(IR, time) = JTotal;
   enddef;

   def comp IR_Degradation as
      var gamma_R: per_s {init: 0.002};
      var IR: dimensionless {pub: in};
      var JDegradation: per_s {pub: out};

      JDegradation = gamma_R*IR;
   enddef;

   def comp SinR_Interface as
      var JTotal: per_s {pub: out};
      var m_1: dimensionless {pub: in};
      var m_3: dimensionless {pub: in};
      var A_R: per_s {init: 0.014};
      var JDegradation: per_s {pub: in};
      var J_IR_Formation: per_s {pub: in};
      var J_R4_Formation: per_s {pub: in};

      JTotal = A_R*(m_1+m_3)-JDegradation-J_IR_Formation-J_R4_Formation*4{dimensionless};
   enddef;

   def comp SinR_Degradation as
      var gamma_R: per_s {init: 0.002};
      var R: dimensionless {pub: in};
      var JDegradation: per_s {pub: out};

      JDegradation = gamma_R*R;
   enddef;

   def comp SinR as
      var time: second {pub: in};
      var JTotal: per_s {pub: in};
      var R: dimensionless {init: 0, pub: out};

      ode(R, time) = JTotal;
   enddef;

   def comp R4_Formation as
      var J_R4_Formation: per_s {pub: out};
      var R: dimensionless {pub: in};
      var R_4: dimensionless {pub: in};
      var k_on_R: per_s {init: 0.00125};
      var k_off_R: per_s {init: 0.5};

      J_R4_Formation = k_on_R*pow(R, 4{dimensionless})-k_off_R*R_4;
   enddef;

   def comp R4_Interface as
      var JTotal: per_s {pub: out};
      var J_R4_Formation: per_s {pub: in};

      JTotal = J_R4_Formation;
   enddef;

   def comp R4 as
      var time: second {pub: in};
      var JTotal: per_s {pub: in};
      var R_4: dimensionless {init: 0, pub: out};

      ode(R_4, time) = JTotal;
   enddef;

   def map between temporalExistence and P1_Transcription for
      vars time and time;
   enddef;

   def map between temporalExistence and P3_Transcription for
      vars time and time;
   enddef;

   def map between temporalExistence and SinI for
      vars time and time;
   enddef;

   def map between temporalExistence and IR for
      vars time and time;
   enddef;

   def map between temporalExistence and SinR for
      vars time and time;
   enddef;

   def map between temporalExistence and R4 for
      vars time and time;
   enddef;

   def map between P1_Transcription and SinI_Interface for
      vars m_1 and m_1;
   enddef;

   def map between P1_Transcription and SinR_Interface for
      vars m_1 and m_1;
   enddef;

   def map between P3_Transcription and SinR_Interface for
      vars m_3 and m_3;
   enddef;

   def map between SinI_Interface and SinI for
      vars JTotal and JTotal;
   enddef;

   def map between SinI and SinI_Degradation for
      vars I and I;
   enddef;

   def map between SinI and IR_Formation for
      vars I and I;
   enddef;

   def map between SinI_Degradation and SinI_Interface for
      vars JDegradation and JDegradation;
   enddef;

   def map between IR_Formation and SinI_Interface for
      vars J_IR_Formation and J_IR_Formation;
   enddef;

   def map between IR_Formation and IR_Interface for
      vars J_IR_Formation and J_IR_Formation;
   enddef;

   def map between IR_Formation and SinR_Interface for
      vars J_IR_Formation and J_IR_Formation;
   enddef;

   def map between IR_Interface and IR for
      vars JTotal and JTotal;
   enddef;

   def map between IR and IR_Formation for
      vars IR and IR;
   enddef;

   def map between IR and IR_Degradation for
      vars IR and IR;
   enddef;

   def map between IR_Degradation and IR_Interface for
      vars JDegradation and JDegradation;
   enddef;

   def map between SinR_Interface and SinR for
      vars JTotal and JTotal;
   enddef;

   def map between SinR and IR_Formation for
      vars R and R;
   enddef;

   def map between SinR and SinR_Degradation for
      vars R and R;
   enddef;

   def map between SinR and R4_Formation for
      vars R and R;
   enddef;

   def map between SinR_Degradation and SinR_Interface for
      vars JDegradation and JDegradation;
   enddef;

   def map between R4_Formation and SinR_Interface for
      vars J_R4_Formation and J_R4_Formation;
   enddef;

   def map between R4_Formation and R4_Interface for
      vars J_R4_Formation and J_R4_Formation;
   enddef;

   def map between R4_Interface and R4 for
      vars JTotal and JTotal;
   enddef;

   def map between R4 and R4_Formation for
      vars R_4 and R_4;
   enddef;

   def map between R4 and P1_Promoter_Activity for
      vars R_4 and R_4;
   enddef;

   def map between P1_Promoter_Activity and P1_Transcription for
      vars alpha_1 and alpha_1;
   enddef;
enddef;