// Created by libAntimony v2.13.0
function Function_for_STATP2n_Formation(k5, TJ, STAT, K_5)
  k5*TJ*STAT/(2*(K_5 + STAT));
end

Function_for_STATP2n_Formation is "Function_for_STATP2n_Formation"

function Function_for_TNFa_mRNA_Degradation(TNFam, t_9)
  TNFam*(ln(2)/t_9);
end

Function_for_TNFa_mRNA_Degradation is "Function_for_TNFa_mRNA_Degradation"

function Function_for_STAT_mRNA_Induction(r_4, IC1, k_26, STATP2n, IC2)
  (r_4*IC1 + k_26*STATP2n)*IC2;
end

Function_for_STAT_mRNA_Induction is "Function_for_STAT_mRNA_Induction"

function Function_for_IFNBenv_Turnover(gamma_, C, vmax2, IFNBm, K_2)
  gamma_*C*vmax2*IFNBm/(K_2 + IFNBm);
end

Function_for_IFNBenv_Turnover is "Function_for_IFNBenv_Turnover"

function Function_for_SOCS_mRNA_Degradation(SOCSm, t_4)
  SOCSm*(ln(2)/t_4);
end

Function_for_SOCS_mRNA_Degradation is "Function_for_SOCS_mRNA_Degradation"

function Function_for_IFNaenv_Translation_Secretion(gamma_, C, vmax_17, IFNam, K_17)
  gamma_*C*vmax_17*IFNam/(K_17 + IFNam);
end

Function_for_IFNaenv_Translation_Secretion is "Function_for_IFNaenv_Translation_Secretion"

function Function_for_STATP2n_Dephosphorylation(STATP2n, t3)
  STATP2n*(ln(2)/t3);
end

Function_for_STATP2n_Dephosphorylation is "Function_for_STATP2n_Dephosphorylation"

function Function_for_IFNb_mRNA_Turnover(r0, IC1, k15, IRF7Pn, IC2)
  (r0*IC1 + k15*IRF7Pn)*IC2;
end

Function_for_IFNb_mRNA_Turnover is "Function_for_IFNb_mRNA_Turnover"

function Function_for_SOCS_mRNA_Induction(r_3, IC1, k_8, STATP2n, IC2)
  (r_3*IC1 + k_8*STATP2n)*IC2;
end

Function_for_SOCS_mRNA_Induction is "Function_for_SOCS_mRNA_Induction"

function Function_for_IFNa_mRNA_Induction(k_16, IRF7Pn, IC2)
  k_16*IRF7Pn*IC2;
end

Function_for_IFNa_mRNA_Induction is "Function_for_IFNa_mRNA_Induction"

function Function_for_IFNb_mRNA_Degradation(IFNBm, t1)
  IFNBm*(ln(2)/t1);
end

Function_for_IFNb_mRNA_Degradation is "Function_for_IFNb_mRNA_Degradation"

function Function_for_STAT_Translation(k_26, STATm)
  k_26*STATm;
end

Function_for_STAT_Translation is "Function_for_STAT_Translation"

function Function_for_IRF7_Translation(k_12, IRF7m, IC1)
  k_12*IRF7m*IC1;
end

Function_for_IRF7_Translation is "Function_for_IRF7_Translation"

function Function_for_IFNa_mRNA_Degradation(IFNam, t_8)
  IFNam*(ln(2)/t_8);
end

Function_for_IFNa_mRNA_Degradation is "Function_for_IFNa_mRNA_Degradation"

function Function_for_TNFa_Translation_Secretion(gamma_, C, vmax_19, TFNam, K_19)
  gamma_*C*vmax_19*TFNam/(K_19 + TFNam);
end

Function_for_TNFa_Translation_Secretion is "Function_for_TNFa_Translation_Secretion"

function Function_for_STAT_mRNA_Degradation(STATm, t_12)
  STATm*(ln(2)/t_12);
end

Function_for_STAT_mRNA_Degradation is "Function_for_STAT_mRNA_Degradation"

function Function_for_TNFa_mRNA_Induction(IC2, r_1, IC1, r_20, TNFenv, K_20)
  IC2*(r_1*IC1 + r_20*TNFenv/(K_20 + TNFenv));
end

Function_for_TNFa_mRNA_Induction is "Function_for_TNFa_mRNA_Induction"

function Function_for_IRF7_mRNA_Degradation(IRF7m, t_6)
  IRF7m*(ln(2)/t_6);
end

Function_for_IRF7_mRNA_Degradation is "Function_for_IRF7_mRNA_Degradation"

function Function_for_IRF7_mRNA_Induction(k_11, STATP2n, k_14, IRF7Pn, IC2)
  (k_11*STATP2n + k_14*IRF7Pn)*IC2;
end

Function_for_IRF7_mRNA_Induction is "Function_for_IRF7_mRNA_Induction"

function Function_for_STAT_Degradation(STAT, t_13)
  STAT*(ln(2)/t_13);
end

Function_for_STAT_Degradation is "Function_for_STAT_Degradation"


model *Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response()

  // Compartments and Species:
  compartment compartment_;
  species IFNBm in compartment_, IFNBenv in compartment_, STATP2n in compartment_;
  species SOCSm in compartment_, IRF7m in compartment_, IRF7Pn in compartment_;
  species IFNam in compartment_, IFNaenv in compartment_, TNFam in compartment_;
  species TFNenv in compartment_, STATm in compartment_, STAT in compartment_;

  // Assignment Rules:
  v_max217 := 20.1*3600;
  k_14 := 3600*8.9e-11;
  v_max19 := 46*3600;
  k_26 := 3600*5e-6;
  sv := 0.1/0.3;
  TJ := (TJ_tot/(1 + K_9*SOCSm/delta))*((IFNBenv + IFNaenv)/(K_3 + IFNBenv + IFNaenv));
  IC1 := (1 + sp*(NS/delta_1)^n_1)/(1 + (NS/delta_1)^n_1);
  NS := r_5*time^n_3/(b_m^n_3 + time^n_3);
  IC2 := (1 + sv*(NS/delta_2)^n_2)/(1 + (NS/delta_2)^n_2);
  gamma_ := 1000000000/6.023e23;

  // Reactions:
  IFNb_mRNA_Induction:  => IFNBm; compartment_*Function_for_IFNb_mRNA_Turnover(r_0, IC1, k_15, IRF7Pn, IC2);
  IFNb_mRNA_Degradation: IFNBm => ; compartment_*Function_for_IFNb_mRNA_Degradation(IFNBm, t_1);
  IFNBenv_Translation_Secretion:  => IFNBenv; compartment_*Function_for_IFNBenv_Turnover(gamma_, C, v_max217, IFNBenv, K_217);
  STATP2n_Formation:  => STATP2n; compartment_*Function_for_STATP2n_Formation(k_5, TJ, STAT, K_5);
  STATP2n_Dephosphorylation: STATP2n => ; compartment_*Function_for_STATP2n_Dephosphorylation(STATP2n, t_3);
  SOCS_mRNA_Induction:  => SOCSm; compartment_*Function_for_SOCS_mRNA_Induction(r_3, IC1, k_8, STATP2n, IC2);
  SOCS_mRNA_Degradation: SOCSm => ; compartment_*Function_for_SOCS_mRNA_Degradation(SOCSm, t_4);
  IRF7_mRNA_Induction:  => IRF7m; compartment_*Function_for_IRF7_mRNA_Induction(k_11, STATP2n, k_14, IRF7Pn, IC2);
  IRF7_mRNA_Degradation: IRF7m => ; compartment_*Function_for_IRF7_mRNA_Degradation(IRF7m, t_6);
  IRF7_Translation:  => IRF7Pn; compartment_*Function_for_IRF7_Translation(k_12, IRF7m, IC1);
  IFNa_mRNA_Induction:  => IFNam; compartment_*Function_for_IFNa_mRNA_Induction(k_16, IRF7Pn, IC2);
  IFNa_mRNA_Degradation: IFNam => ; compartment_*Function_for_IFNa_mRNA_Degradation(IFNam, t_8);
  IFNaenv_Translation_Secretion:  => IFNaenv; compartment_*Function_for_IFNaenv_Translation_Secretion(gamma_, C, v_max217, IFNam, K_217);
  TNFa_mRNA_Induction:  => TNFam; compartment_*Function_for_TNFa_mRNA_Induction(IC2, r_1, IC1, r_20, TFNenv, K_20);
  TNFa_mRNA_Degradation: TNFam => ; compartment_*Function_for_TNFa_mRNA_Degradation(TNFam, t_9);
  TNFa_Translation_Secretion:  => TFNenv; compartment_*Function_for_TNFa_Translation_Secretion(gamma_, C, v_max19, TNFam, K_19);
  STAT_mRNA_Induction:  => STATm; compartment_*Function_for_STAT_mRNA_Induction(r_4, IC1, k_26, STATP2n, IC2);
  STAT_mRNA_Degradation: STATm => ; compartment_*Function_for_STAT_mRNA_Degradation(STATm, t_12);
  STAT_Translation:  => STAT; compartment_*Function_for_STAT_Translation(k_28, STATm);
  STAT_Degradation: STAT => ; compartment_*Function_for_STAT_Degradation(STAT, t_13);

  // Species initializations:
  IFNBm = 1;
  IFNBenv = 1;
  STATP2n = 1;
  SOCSm = 1;
  IRF7m = 1;
  IRF7Pn = 1;
  IFNam = 1;
  IFNaenv = 1;
  TNFam = 1;
  TFNenv = 1;
  STATm = 1;
  STAT = 1;

  // Compartment initializations:
  compartment_ = 1;

  // Variable initializations:
  r_0 = 0.001;
  k_15 = 3.6e-05;
  t_1 = 2.5;
  K_217 = 0.002;
  TJ_tot = 0.0001;
  K_3 = 0.0043;
  d = 0.0003;
  K_9 = 780;
  k_5 = 3600;
  K_5 = 0.01;
  t_3 = 0.56;
  r_3 = 1e-07;
  k_8 = 0.0036;
  t_4 = 0.46;
  k_11 = 0.00036;
  t_6 = 1;
  k_12 = 360;
  k_16 = 0.36;
  t_8 = 2;
  r_1 = 0.0001;
  r_20 = 0.001;
  K_20 = 0.0006;
  t_9 = 2;
  K_19 = 0.004;
  r_4 = 1e-06;
  t_12 = 1;
  k_28 = 360;
  t_13 = 15;
  r_5 = 1;
  n_3 = 5;
  b_m = 6;
  sp = 0.3;
  d_1 = 0.1;
  n_1 = 1;
  d_2 = 0.4;
  n_2 = 5;
  delta = 0.0003;
  delta_1 = 0.1;
  delta_2 = 0.4;
  C = 500000;

  // Other declarations:
  var v_max217, k_14, v_max19, k_26, sv, TJ, IC1, NS, IC2, gamma_;
  const compartment_, r_0, k_15, t_1, K_217, TJ_tot, K_3, d, K_9, k_5, K_5;
  const t_3, r_3, k_8, t_4, k_11, t_6, k_12, k_16, t_8, r_1, r_20, K_20, t_9;
  const K_19, r_4, t_12, k_28, t_13, r_5, n_3, b_m, sp, d_1, n_1, d_2, n_2;
  const delta, delta_1, delta_2, C;

  // Unit definitions:
  unit time_unit = 3600 second;
  unit substance = 1e-6 mole;

  // Display Names:
  time_unit is "time";
  compartment_ is "compartment";
  gamma_ is "gamma";

  // SBO terms:
  IFNb_mRNA_Induction.sboTerm = 183
  IFNb_mRNA_Degradation.sboTerm = 179
  IFNBenv_Translation_Secretion.sboTerm = 184
  SOCS_mRNA_Induction.sboTerm = 183
  SOCS_mRNA_Degradation.sboTerm = 179
  IRF7_mRNA_Induction.sboTerm = 183
  IRF7_mRNA_Degradation.sboTerm = 179
  IRF7_Translation.sboTerm = 184
  IFNa_mRNA_Induction.sboTerm = 183
  IFNa_mRNA_Degradation.sboTerm = 179
  IFNaenv_Translation_Secretion.sboTerm = 184
  TNFa_mRNA_Induction.sboTerm = 183
  TNFa_mRNA_Degradation.sboTerm = 179
  TNFa_Translation_Secretion.sboTerm = 184
  STAT_mRNA_Induction.sboTerm = 183
  STAT_mRNA_Degradation.sboTerm = 179
  STAT_Translation.sboTerm = 184
  STAT_Degradation.sboTerm = 179

  // CV terms:
  compartment_ hypernym "http://identifiers.org/ncit/C13356"
  IFNBm encodement "http://identifiers.org/ncit/C20495"
  IFNBenv identity "http://identifiers.org/ncit/C20495"
  STATP2n part "http://identifiers.org/ncit/C19618"
  STATP2n property "http://identifiers.org/sbo/SBO:0000607"
  SOCSm encodement "http://identifiers.org/ncit/C97796"
  IRF7m encodement "http://identifiers.org/ncit/C128883"
  IRF7Pn hypernym "http://identifiers.org/ncit/C128883"
  IFNam encodement "http://identifiers.org/ncit/C20494"
  IFNaenv identity "http://identifiers.org/ncit/C20494"
  TNFam encodement "http://identifiers.org/pr/PR:000000134"
  TFNenv identity "http://identifiers.org/pr/PR:000000134"
  STATm encodement "http://identifiers.org/ncit/C19618"
  STAT identity "http://identifiers.org/ncit/C19618"
  IFNb_mRNA_Induction identity "http://identifiers.org/sbo/SBO:0000183"
  IFNb_mRNA_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
  IFNBenv_Translation_Secretion identity "http://identifiers.org/sbo/SBO:0000184"
  STATP2n_Formation hypernym "http://identifiers.org/ncit/C97201"
  STATP2n_Dephosphorylation identity "http://identifiers.org/ncit/C20612"
  SOCS_mRNA_Induction identity "http://identifiers.org/sbo/SBO:0000183"
  SOCS_mRNA_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
  IRF7_mRNA_Induction identity "http://identifiers.org/sbo/SBO:0000183"
  IRF7_mRNA_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
  IRF7_Translation identity "http://identifiers.org/sbo/SBO:0000184"
  IFNa_mRNA_Induction identity "http://identifiers.org/sbo/SBO:0000183"
  IFNa_mRNA_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
  IFNaenv_Translation_Secretion identity "http://identifiers.org/sbo/SBO:0000184"
  TNFa_mRNA_Induction identity "http://identifiers.org/sbo/SBO:0000183"
  TNFa_mRNA_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
  TNFa_Translation_Secretion identity "http://identifiers.org/sbo/SBO:0000184"
  STAT_mRNA_Induction identity "http://identifiers.org/sbo/SBO:0000183"
  STAT_mRNA_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
  STAT_Translation identity "http://identifiers.org/sbo/SBO:0000184"
  STAT_Degradation identity "http://identifiers.org/sbo/SBO:0000179"
end

Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response is "Fribourg2014 - Model of influenza A virus infection dynamics of viral antagonism and innate immune response."

Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response description "http://identifiers.org/pubmed/24594370"
Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response model_entity_is "http://identifiers.org/biomodels.db/MODEL1912120001",
                                                                                                                            "http://identifiers.org/biomodels.db/BIOMD0000000889"
Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response property "http://identifiers.org/ncit/C18011"
Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response property "http://identifiers.org/mamo/MAMO_0000046"
Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response property "http://identifiers.org/pr/PR:000044797"
Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response property "http://identifiers.org/ncit/C20493"
Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response taxon "http://identifiers.org/taxonomy/9606"
