// Created by libAntimony v2.13.0
function Function_for_the_infection_of_normal_cell(beta, x, v)
  beta*x*v;
end

Function_for_the_infection_of_normal_cell is "Function for the infection of normal cell"

function Constant_flux__irreversible(v)
  v;
end

Constant_flux__irreversible is "Constant flux (irreversible)"

function Funtion_for_the_infection_of_single_infected_cel(alpha, w, y)
  alpha*w*y;
end

Funtion_for_the_infection_of_single_infected_cel is "Funtion for the infection of single infected cel"

function Function_for_the_release_of_the_pathogen(k, y)
  k*y;
end

Function_for_the_release_of_the_pathogen is "Function for the release of the pathogen"

function Function_for_the_release_of_recombinant_virus(c, z)
  c*z;
end

Function_for_the_release_of_recombinant_virus is "Function for the release of recombinant virus"


model *New_Model()

  // Compartments and Species:
  compartment Plasma;
  species Normal_Th_cells in Plasma, Pathogen_Virus in Plasma, Single_Infected_Th_Cells in Plasma;
  species Recombinant_Virus in Plasma, Double_Infected_Th_Cells in Plasma;

  // Reactions:
  Production_of_Normal_cells:  => Normal_Th_cells; Plasma*Constant_flux__irreversible(lamda);
  Degradation_of_Normal_cells: Normal_Th_cells => ; Plasma*d*Normal_Th_cells;
  Infection_of_Normal_cells_with_Pathogen: Normal_Th_cells => Single_Infected_Th_Cells; Plasma*Function_for_the_infection_of_normal_cell(beta, Normal_Th_cells, Pathogen_Virus);
  Degradation_of_Single_Infected_Cells: Single_Infected_Th_Cells => ; Plasma*a*Single_Infected_Th_Cells;
  Infection_of_Single_Infeced_Cells_with_Recombinant_Virus: Single_Infected_Th_Cells => Double_Infected_Th_Cells; Plasma*Funtion_for_the_infection_of_single_infected_cel(alpha, Recombinant_Virus, Single_Infected_Th_Cells);
  Release_of_Pathogen:  => Pathogen_Virus; Plasma*Function_for_the_release_of_the_pathogen(k, Single_Infected_Th_Cells);
  Degradation_of_Double_Infected_Cells: Double_Infected_Th_Cells => ; Plasma*b*Double_Infected_Th_Cells;
  Release_of_Recombinant_Virus:  => Recombinant_Virus; Plasma*Function_for_the_release_of_recombinant_virus(c, Double_Infected_Th_Cells);
  Degradation_of_Pathogen_Virus: Pathogen_Virus => ; Plasma*u*Pathogen_Virus;
  Degradation_of_Recombinant_Virus: Recombinant_Virus => ; Plasma*q*Recombinant_Virus;

  // Species initializations:
  Normal_Th_cells = 3;
  Pathogen_Virus = 149;
  Single_Infected_Th_Cells = 6;
  Recombinant_Virus = 1;
  Double_Infected_Th_Cells = 0;

  // Compartment initializations:
  Plasma = 1;

  // Variable initializations:
  d = 0.01;
  lamda = 2;
  beta = 0.004;
  a = 0.33;
  alpha = 0.004;
  b = 2;
  k = 50;
  u = 2;
  c = 2000;
  q = 2;

  // Other declarations:
  const Plasma, d, lamda, beta, a, alpha, b, k, u, c, q;

  // Unit definitions:
  unit time_unit = 86400 second;

  // Display Names:
  time_unit is "time";
  Normal_Th_cells is "Normal Th cells";
  Pathogen_Virus is "Pathogen Virus";
  Single_Infected_Th_Cells is "Single Infected Th Cells";
  Recombinant_Virus is "Recombinant Virus";
  Double_Infected_Th_Cells is "Double Infected Th Cells";
  Production_of_Normal_cells is "Production of Normal cells";
  Degradation_of_Normal_cells is "Degradation of Normal cells";
  Infection_of_Normal_cells_with_Pathogen is "Infection of Normal cells with Pathogen";
  Degradation_of_Single_Infected_Cells is "Degradation of Single Infected Cells";
  Infection_of_Single_Infeced_Cells_with_Recombinant_Virus is "Infection of Single Infeced Cells with Recombinant Virus";
  Release_of_Pathogen is "Release of Pathogen";
  Degradation_of_Double_Infected_Cells is "Degradation of Double Infected Cells";
  Release_of_Recombinant_Virus is "Release of Recombinant Virus";
  Degradation_of_Pathogen_Virus is "Degradation of Pathogen Virus";
  Degradation_of_Recombinant_Virus is "Degradation of Recombinant Virus";

  // CV terms:
  Plasma hypernym "http://identifiers.org/ncit/C13356"
  Normal_Th_cells identity "http://identifiers.org/bto/BTO:0002417"
  Pathogen_Virus hypernym "http://identifiers.org/taxonomy/11676"
  Single_Infected_Th_Cells hypernym "http://identifiers.org/bto/BTO:0002417"
  Single_Infected_Th_Cells hypernym "http://identifiers.org/bto/BTO:0000152"
  Recombinant_Virus hypernym "http://identifiers.org/ncit/C97158"
  Recombinant_Virus hypernym "http://identifiers.org/taxonomy/10239"
  Double_Infected_Th_Cells hypernym "http://identifiers.org/bto/BTO:0000152"
  Double_Infected_Th_Cells hypernym "http://identifiers.org/bto/BTO:0002417"
  Production_of_Normal_cells hypernym "http://identifiers.org/ncit/C61408"
  Degradation_of_Normal_cells hypernym "http://identifiers.org/sbo/SBO:0000179"
  Infection_of_Normal_cells_with_Pathogen hypernym "http://identifiers.org/ncit/C128320"
  Degradation_of_Single_Infected_Cells hypernym "http://identifiers.org/sbo/SBO:0000179"
  Infection_of_Single_Infeced_Cells_with_Recombinant_Virus hypernym "http://identifiers.org/ncit/C128320"
  Release_of_Pathogen hypernym "http://identifiers.org/go/GO:0019076"
  Degradation_of_Double_Infected_Cells hypernym "http://identifiers.org/sbo/SBO:0000179"
  Release_of_Recombinant_Virus hypernym "http://identifiers.org/go/GO:0019076"
  Degradation_of_Pathogen_Virus hypernym "http://identifiers.org/sbo/SBO:0000179"
  Degradation_of_Recombinant_Virus hypernym "http://identifiers.org/sbo/SBO:0000179"
end

New_Model is "Revilla2003 - Controlling HIV infection using recombinant viruses"

New_Model model_entity_is "http://identifiers.org/biomodels.db/MODEL1006230047",
                          "http://identifiers.org/biomodels.db/BIOMD0000000707"
New_Model container "http://identifiers.org/bto/BTO:0002417"
New_Model property "http://identifiers.org/efo/0000764"
New_Model property "http://identifiers.org/efo/0000727"
New_Model property "http://identifiers.org/mamo/MAMO_0000046"
New_Model taxon "http://identifiers.org/taxonomy/9606"
New_Model taxon "http://identifiers.org/taxonomy/11676"
New_Model description "http://identifiers.org/pubmed/12941536"
