// Created by libAntimony v2.13.0
function Function_for_Reaction_1__2(gammaV, I)
  gammaV*I;
end

Function_for_Reaction_1__2 is "Function for Reaction 1 [2]"

function Function_for_Reaction_2__2(gammaVA, S, A, V)
  gammaVA*S*A*V;
end

Function_for_Reaction_2__2 is "Function for Reaction 2 [2]"

function Function_for_Reaction_3__2(gammaVH, H, V)
  gammaVH*H*V;
end

Function_for_Reaction_3__2 is "Function for Reaction 3 [2]"

function Function_for_Reaction_5__1(aV1, V, aV2)
  aV1*V/(1 + aV2*V);
end

Function_for_Reaction_5__1 is "Function for Reaction 5 [1]"

function Function_for_Reaction_6__1(bHD, D, H, R)
  bHD*D*(H + R);
end

Function_for_Reaction_6__1 is "Function for Reaction 6 [1]"

function Function_for_Reaction_8(V, H, gammaHV)
  gammaHV*V*H;
end

Function_for_Reaction_8 is "Function for Reaction 8"

function Function_for_Reaction_9__1(bHF, F, H)
  bHF*F*H;
end

Function_for_Reaction_9__1 is "Function for Reaction 9 [1]"

function Function_for_Reaction_10(bIE, E, I)
  bIE*E*I;
end

Function_for_Reaction_10 is "Function for Reaction 10"

function Function_for_Reaction_12(bMD, D, bMV, V, M)
  (bMD*D + bMV*V)*(1 - M);
end

Function_for_Reaction_12 is "Function for Reaction 12"

function Function_for_Reaction_14(bF, M)
  bF*M;
end

Function_for_Reaction_14 is "Function for Reaction 14"

function Function_for_Reaction_15(cF, I)
  cF*I;
end

Function_for_Reaction_15 is "Function for Reaction 15"

function Function_for_Reaction_16(bFH, H, F)
  bFH*H*F;
end

Function_for_Reaction_16 is "Function for Reaction 16"

function Function_for_Reaction_18(bEM, M, E)
  bEM*M*E;
end

Function_for_Reaction_18 is "Function for Reaction 18"

function Function_for_Reaction_19(bEI, I, E)
  bEI*I*E;
end

Function_for_Reaction_19 is "Function for Reaction 19"

function Function_for_Reaction_20(aE, E)
  aE*(E - 1);
end

Function_for_Reaction_20 is "Function for Reaction 20"

function Function_for_Reaction_21(M, P, bPM)
  bPM*M*P;
end

Function_for_Reaction_21 is "Function for Reaction 21"

function Function_for_Reaction_22(aP, P)
  aP*(P - 1);
end

Function_for_Reaction_22 is "Function for Reaction 22"

function Function_for_Reaction_23(bA, P)
  bA*P;
end

Function_for_Reaction_23 is "Function for Reaction 23"

function Function_for_Reaction_24(gammaAV, S, A, V)
  gammaAV*S*A*V;
end

Function_for_Reaction_24 is "Function for Reaction 24"

function Function_for_Reaction_26(r, P, S)
  r*P*(1 - S);
end

Function_for_Reaction_26 is "Function for Reaction 26"


model *Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection()

  // Compartments and Species:
  compartment Respiratory_tract_mucosa;
  species Viral_Load__V in Respiratory_tract_mucosa, Healthy_Epithelial_cells__H in Respiratory_tract_mucosa;
  species Infected_Epithelial_cells__I in Respiratory_tract_mucosa, APC_cells__M in Respiratory_tract_mucosa;
  species Interferons__F in Respiratory_tract_mucosa, Resistant_cells__R in Respiratory_tract_mucosa;
  species Effector_cells__E in Respiratory_tract_mucosa, Plasma_cells__P in Respiratory_tract_mucosa;
  species Antibodies__A in Respiratory_tract_mucosa, Antigenic_compatibility__S in Respiratory_tract_mucosa;
  species $Dead_cells__D in Respiratory_tract_mucosa;

  // Assignment Rules:
  Dead_cells__D := 1 - Healthy_Epithelial_cells__H - Resistant_cells__R - Infected_Epithelial_cells__I;

  // Reactions:
  Secretion_of_Virus__V__by_Infected_epithelial_cells__I:  => Viral_Load__V; Respiratory_tract_mucosa*Function_for_Reaction_1__2(gammaV, Infected_Epithelial_cells__I);
  Neutralization_of_Virus__V__by_Antibody__A: Viral_Load__V => ; Respiratory_tract_mucosa*Function_for_Reaction_2__2(gammaVA, Antigenic_compatibility__S, Antibodies__A, Viral_Load__V);
  Adsorption_of_Virus__V__by_Healthy_epithelial_cells__H: Viral_Load__V => ; Respiratory_tract_mucosa*Function_for_Reaction_3__2(gammaVH, Healthy_Epithelial_cells__H, Viral_Load__V);
  Non_Specific_Removal_of_Virus__V___alphaV: Viral_Load__V => ; Respiratory_tract_mucosa*alphaV*Viral_Load__V;
  Non_Specific_Removal_of_Virus__V___aV1_aV2: Viral_Load__V => ; Respiratory_tract_mucosa*Function_for_Reaction_5__1(aV1, Viral_Load__V, aV2);
  Regeneration_of_Healthy_Epithelial_cells__H:  => Healthy_Epithelial_cells__H; Respiratory_tract_mucosa*Function_for_Reaction_6__1(bHD, Dead_cells__D, Healthy_Epithelial_cells__H, Resistant_cells__R);
  R_virus_resistant_state_decay: Resistant_cells__R => Healthy_Epithelial_cells__H; Respiratory_tract_mucosa*aR*Resistant_cells__R;
  Infection_of_Healthy_Epithelial_cells_by__V: Healthy_Epithelial_cells__H => Infected_Epithelial_cells__I; Respiratory_tract_mucosa*Function_for_Reaction_8(Viral_Load__V, Healthy_Epithelial_cells__H, gammaHV);
  H_virus_resistant_state_induction: Healthy_Epithelial_cells__H => Resistant_cells__R; Respiratory_tract_mucosa*Function_for_Reaction_9__1(bHF, Interferons__F, Healthy_Epithelial_cells__H);
  Degradation_of_Infected_Epithelial_cells___E: Infected_Epithelial_cells__I => ; Respiratory_tract_mucosa*Function_for_Reaction_10(bIE, Effector_cells__E, Infected_Epithelial_cells__I);
  Degradation_of_Infected_Epithelial_cells___Cytopathicity_of_V: Infected_Epithelial_cells__I => ; Respiratory_tract_mucosa*aI*Infected_Epithelial_cells__I;
  Stimulation_of_APC_cells__M__by_Dead_cells__D__and_Virus__V:  => APC_cells__M; Respiratory_tract_mucosa*Function_for_Reaction_12(bMD, Dead_cells__D, bMV, Viral_Load__V, APC_cells__M);
  Stimulates_State_loss_of_APC_cells__M: APC_cells__M => ; Respiratory_tract_mucosa*aM*APC_cells__M;
  Synthesis_of_Interferons__F___M:  => Interferons__F; Respiratory_tract_mucosa*Function_for_Reaction_14(bF, APC_cells__M);
  Synthesis_of_Interferons__F___I:  => Interferons__F; Respiratory_tract_mucosa*Function_for_Reaction_15(cF, Infected_Epithelial_cells__I);
  Binding_of_Healthy_epithelial_cells__H__and_Interferons__F: Interferons__F => ; Respiratory_tract_mucosa*Function_for_Reaction_16(bFH, Healthy_Epithelial_cells__H, Interferons__F);
  Degradation_of_Interferons__F: Interferons__F => ; Respiratory_tract_mucosa*aF*Interferons__F;
  Stimulation_of_Effector_cells__E___M:  => Effector_cells__E; Respiratory_tract_mucosa*Function_for_Reaction_18(bEM, APC_cells__M, Effector_cells__E);
  Degradation_of_Effector_cells__E___Mod_I: Effector_cells__E => ; Respiratory_tract_mucosa*Function_for_Reaction_19(bEI, Infected_Epithelial_cells__I, Effector_cells__E);
  Degradation_of_Effector_cells__E: Effector_cells__E => ; Respiratory_tract_mucosa*Function_for_Reaction_20(Degradation_of_Effector_cells__E_aE, Effector_cells__E);
  Synthesis_of_Plasma_cells__P___Mod_M:  => Plasma_cells__P; Respiratory_tract_mucosa*Function_for_Reaction_21(APC_cells__M, Plasma_cells__P, bPM);
  Degradation_of_Plasma_cells__P: Plasma_cells__P => ; Respiratory_tract_mucosa*Function_for_Reaction_22(aP, Plasma_cells__P);
  Synthesis_of_Antibody__A___Mod_P:  => Antibodies__A; Respiratory_tract_mucosa*Function_for_Reaction_23(bA, Plasma_cells__P);
  Binding_of_Antibody__A__and_Virus__V: Antibodies__A => ; Respiratory_tract_mucosa*Function_for_Reaction_24(gammaAV, Antigenic_compatibility__S, Antibodies__A, Viral_Load__V);
  Degradation_of_Antibody__A: Antibodies__A => ; Respiratory_tract_mucosa*aA*Antibodies__A;
  Antigenic_Compatibility_variable:  => Antigenic_compatibility__S; Respiratory_tract_mucosa*Function_for_Reaction_26(r, Plasma_cells__P, Antigenic_compatibility__S);

  // Events:
  Event_to_keep_viral_load_non_negative: at Viral_Load__V < 0: Viral_Load__V = 0;

  // Species initializations:
  Viral_Load__V = 0.01;
  Healthy_Epithelial_cells__H = 1;
  Infected_Epithelial_cells__I = 0;
  APC_cells__M = 0;
  Interferons__F = 0;
  Resistant_cells__R = 0;
  Effector_cells__E = 1;
  Plasma_cells__P = 1;
  Antibodies__A = 1;
  Antigenic_compatibility__S = 0.1;

  // Compartment initializations:
  Respiratory_tract_mucosa = 1;

  // Variable initializations:
  gammaV = 510;
  gammaVA = 619.2;
  gammaVH = 1.02;
  alphaV = 1.7;
  aV1 = 100;
  aV2 = 23000;
  bHD = 4;
  aR = 1;
  gammaHV = 0.34;
  bHF = 0.01;
  bIE = 0.066;
  aI = 1.5;
  bMD = 1;
  bMV = 0.0037;
  aM = 1;
  bF = 250000;
  cF = 2000;
  bFH = 17;
  aF = 8;
  bEM = 8.3;
  bEI = 2.72;
  aE = 0.4;
  bPM = 11.5;
  aP = 0.4;
  bA = 0.043;
  gammaAV = 146.25;
  aA = 0.043;
  r = 3e-05;
  Degradation_of_Effector_cells__E_aE = 0.1;

  // Other declarations:
  const Respiratory_tract_mucosa, gammaV, gammaVA, gammaVH, alphaV, aV1, aV2;
  const bHD, aR, gammaHV, bHF, bIE, aI, bMD, bMV, aM, bF, cF, bFH, aF, bEM;
  const bEI, aE, bPM, aP, bA, gammaAV, aA, r;

  // Unit definitions:
  unit volume = 1e-3 litre;
  unit time_unit = 86400 second;
  unit substance = 1e-3 mole;

  // Display Names:
  time_unit is "time";
  Respiratory_tract_mucosa is "Respiratory tract mucosa";
  Viral_Load__V is "Viral Load (V)";
  Healthy_Epithelial_cells__H is "Healthy Epithelial cells (H)";
  Infected_Epithelial_cells__I is "Infected Epithelial cells (I)";
  APC_cells__M is "APC cells (M)";
  Interferons__F is "Interferons (F)";
  Resistant_cells__R is "Resistant cells (R)";
  Effector_cells__E is "Effector cells (E)";
  Plasma_cells__P is "Plasma cells (P)";
  Antibodies__A is "Antibodies (A)";
  Antigenic_compatibility__S is "Antigenic compatibility (S)";
  Dead_cells__D is "Dead cells (D)";
  Event_to_keep_viral_load_non_negative is "Event to keep viral load non-negative";
  Secretion_of_Virus__V__by_Infected_epithelial_cells__I is "Secretion of Virus (V) by Infected epithelial cells (I)";
  Neutralization_of_Virus__V__by_Antibody__A is "Neutralization of Virus (V) by Antibody (A)";
  Adsorption_of_Virus__V__by_Healthy_epithelial_cells__H is "Adsorption of Virus (V) by Healthy epithelial cells (H)";
  Non_Specific_Removal_of_Virus__V___alphaV is "Non-Specific Removal of Virus (V) [alphaV]";
  Non_Specific_Removal_of_Virus__V___aV1_aV2 is "Non-Specific Removal of Virus (V) [aV1 aV2]";
  Regeneration_of_Healthy_Epithelial_cells__H is "Regeneration of Healthy Epithelial cells (H)";
  R_virus_resistant_state_decay is "R virus resistant state decay";
  Infection_of_Healthy_Epithelial_cells_by__V is "Infection of Healthy Epithelial cells by (V)";
  H_virus_resistant_state_induction is "H virus resistant state induction";
  Degradation_of_Infected_Epithelial_cells___E is "Degradation of Infected Epithelial cells  [E]";
  Degradation_of_Infected_Epithelial_cells___Cytopathicity_of_V is "Degradation of Infected Epithelial cells  [Cytopathicity of V]";
  Stimulation_of_APC_cells__M__by_Dead_cells__D__and_Virus__V is "Stimulation of APC cells (M) by Dead cells (D) and Virus (V)";
  Stimulates_State_loss_of_APC_cells__M is "Stimulates State loss of APC cells (M)";
  Synthesis_of_Interferons__F___M is "Synthesis of Interferons (F) [M]";
  Synthesis_of_Interferons__F___I is "Synthesis of Interferons (F) [I]";
  Binding_of_Healthy_epithelial_cells__H__and_Interferons__F is "Binding of Healthy epithelial cells (H) and Interferons (F)";
  Degradation_of_Interferons__F is "Degradation of Interferons (F)";
  Stimulation_of_Effector_cells__E___M is "Stimulation of Effector cells (E) [M]";
  Degradation_of_Effector_cells__E___Mod_I is "Degradation of Effector cells (E) [Mod=I]";
  Degradation_of_Effector_cells__E is "Degradation of Effector cells (E)";
  Synthesis_of_Plasma_cells__P___Mod_M is "Synthesis of Plasma cells (P) [Mod=M]";
  Degradation_of_Plasma_cells__P is "Degradation of Plasma cells (P)";
  Synthesis_of_Antibody__A___Mod_P is "Synthesis of Antibody (A) [Mod=P]";
  Binding_of_Antibody__A__and_Virus__V is "Binding of Antibody (A) and Virus (V)";
  Degradation_of_Antibody__A is "Degradation of Antibody (A)";
  Antigenic_Compatibility_variable is "Antigenic Compatibility variable";

  // CV terms:
  Respiratory_tract_mucosa hypernym "http://identifiers.org/bto/BTO:0000973"
  Viral_Load__V identity "http://identifiers.org/ncit/C53454"
  Viral_Load__V taxon "http://identifiers.org/taxonomy/11320"
  Healthy_Epithelial_cells__H hypernym "http://identifiers.org/ncit/C12578"
  Infected_Epithelial_cells__I hypernym "http://identifiers.org/ncit/C12578"
  Infected_Epithelial_cells__I hypernym "http://identifiers.org/bto/BTO:0000152"
  APC_cells__M hypernym "http://identifiers.org/ncit/C12621"
  Interferons__F hypernym "http://identifiers.org/ncit/C20493"
  Resistant_cells__R hypernym "http://identifiers.org/ncit/C12578"
  Resistant_cells__R property "http://identifiers.org/mp/MP:0002410"
  Effector_cells__E hypernym "http://identifiers.org/ncit/C104083"
  Effector_cells__E hypernym "http://identifiers.org/bto/BTO:0000289"
  Plasma_cells__P hypernym "http://identifiers.org/ncit/C12486"
  Antibodies__A identity "http://identifiers.org/efo/0000264"
  Antibodies__A hypernym "http://identifiers.org/ncit/C118191"
  Antigenic_compatibility__S hypernym "http://identifiers.org/omit/0002315"
  Dead_cells__D hypernym "http://identifiers.org/ncit/C12578"
  Dead_cells__D property "http://identifiers.org/go/GO:0008219"
  Dead_cells__D property "http://identifiers.org/ncit/C28554"
  Secretion_of_Virus__V__by_Infected_epithelial_cells__I hypernym "http://identifiers.org/go/GO:0019076"
  Infection_of_Healthy_Epithelial_cells_by__V hypernym "http://identifiers.org/ncit/C128320"
  Degradation_of_Infected_Epithelial_cells___E hypernym "http://identifiers.org/sbo/SBO:0000179"
  Degradation_of_Infected_Epithelial_cells___Cytopathicity_of_V hypernym "http://identifiers.org/sbo/SBO:0000179"
  Synthesis_of_Interferons__F___M hypernym "http://identifiers.org/ncit/C61408"
  Synthesis_of_Interferons__F___I hypernym "http://identifiers.org/ncit/C61408"
  Binding_of_Healthy_epithelial_cells__H__and_Interferons__F hypernym "http://identifiers.org/go/GO:0005488"
  Degradation_of_Interferons__F hypernym "http://identifiers.org/sbo/SBO:0000179"
  Degradation_of_Effector_cells__E___Mod_I hypernym "http://identifiers.org/sbo/SBO:0000179"
  Degradation_of_Effector_cells__E hypernym "http://identifiers.org/sbo/SBO:0000179"
  Synthesis_of_Plasma_cells__P___Mod_M hypernym "http://identifiers.org/ncit/C61408"
  Degradation_of_Plasma_cells__P hypernym "http://identifiers.org/sbo/SBO:0000179"
  Synthesis_of_Antibody__A___Mod_P hypernym "http://identifiers.org/ncit/C61408"
  Binding_of_Antibody__A__and_Virus__V hypernym "http://identifiers.org/go/GO:0005488"
  Degradation_of_Antibody__A hypernym "http://identifiers.org/sbo/SBO:0000179"
end

Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection is "Hancioglu2007 - Human Immune Response to Influenza A virus Infection"

Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection model_entity_is "http://identifiers.org/biomodels.db/MODEL1808280004",
                                                                                     "http://identifiers.org/biomodels.db/BIOMD0000000711"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection property "http://identifiers.org/go/GO:0006955"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection property "http://identifiers.org/go/GO:0002250"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection property "http://identifiers.org/go/GO:0045087"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection property "http://identifiers.org/mamo/MAMO_0000046"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection taxon "http://identifiers.org/taxonomy/11320"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection taxon "http://identifiers.org/taxonomy/9606"
Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection description "http://identifiers.org/pubmed/17266989"
