// Created by libAntimony v2.13.0
function Constant_flux__irreversible(v)
  v;
end

Constant_flux__irreversible is "Constant flux (irreversible)"

function Differentiate_into_effectors_0(c, y, q, w)
  c*q*y*w;
end

Differentiate_into_effectors_0 is "Differentiate into effectors"

function Killed_by_CTL_effectors_0(p, y, z)
  p*y*z;
end

Killed_by_CTL_effectors_0 is "Killed by CTL effectors"

function Proliferation_of_CTLp_0(c, x, y, w)
  c*x*y*w;
end

Proliferation_of_CTLp_0 is "Proliferation of CTLp"

function Drug_therapy_during_primary_phase_of_infection(s, beta, x, y)
  s*beta*x*y;
end

Drug_therapy_during_primary_phase_of_infection is "Drug therapy during primary phase of infection"


model *Wodarz1999_CTL_memory_response_HIV()

  // Compartments and Species:
  compartment COMpartment;
  species w in COMpartment, x in COMpartment, y in COMpartment, z in COMpartment;

  // Assignment Rules:
  log_y := log10(y);
  log_w := log10(w);
  s := piecewise(1, time < 1, piecewise(1, time > 15, 0.0042));

  // Reactions:
  Degradation_of_w: w => ; COMpartment*b*w;
  Degradation_of_x: x => ; COMpartment*d*x;
  Degradation_of_y: y => ; COMpartment*a*y;
  Degradation_of_z: z => ; COMpartment*h*z;
  Differentiate_into_effectors: w => z; COMpartment*Differentiate_into_effectors_0(c, y, q, w);
  Infection_of_x: x => y; COMpartment*Drug_therapy_during_primary_phase_of_infection(s, beta, x, y);
  Killed_by_CTL_effectors: y => ; COMpartment*Killed_by_CTL_effectors_0(p, y, z);
  Production_of_x:  => x; COMpartment*Constant_flux__irreversible(lamda);
  Proliferation_of_CTLp:  => w; COMpartment*Proliferation_of_CTLp_0(c, x, y, w);

  // Species initializations:
  w = 0.001;
  x = 10;
  y = 0.1;
  z = 0;

  // Compartment initializations:
  COMpartment = 1;

  // Variable initializations:
  lamda = 1;
  d = 0.1;
  a = 0.2;
  b = 0.01;
  h = 0.1;
  beta = 1.5;
  p = 1;
  q = 0.5;
  c = 0.1;

  // Other declarations:
  var log_y, log_w, s;
  const COMpartment, lamda, d, a, b, h, beta, p, q, c;

  // Unit definitions:
  unit time_unit = 86400 second;

  // Display Names:
  time_unit is "time";
  COMpartment is "Patient";
  Degradation_of_w is "Degradation of w";
  Degradation_of_x is "Degradation of x";
  Degradation_of_y is "Degradation of y";
  Degradation_of_z is "Degradation of z";
  Differentiate_into_effectors is "Differentiate into effectors";
  Infection_of_x is "Infection of x";
  Killed_by_CTL_effectors is "Killed by CTL effectors";
  Production_of_x is "Production of x";
  Proliferation_of_CTLp is "Proliferation of CTLp";

  // CV terms:
  w hypernym "http://identifiers.org/bto/BTO:0000289"
  w property "http://identifiers.org/efo/0001651"
  x hypernym "http://identifiers.org/ncit/C12537"
  x property "http://identifiers.org/efo/0001460"
  y hypernym "http://identifiers.org/ncit/C12537"
  y property "http://identifiers.org/efo/0000764"
  z hypernym "http://identifiers.org/cl/CL:0000911"
  z hypernym "http://identifiers.org/bto/BTO:0000289"
  lamda hypernym "http://identifiers.org/sbo/SBO:0000610"
  d encodement "http://identifiers.org/go/GO:0008219"
  a encodement "http://identifiers.org/sbo/SBO:0000179"
  b encodement "http://identifiers.org/go/GO:0008219"
  h encodement "http://identifiers.org/go/GO:0008219"
  beta encodement "http://identifiers.org/efo/0000544"
  p encodement "http://identifiers.org/go/GO:0001909"
  q encodement "http://identifiers.org/go/GO:0045065"
  c encodement "http://identifiers.org/go/GO:0046651"
  s encodement "http://identifiers.org/go/GO:0042493"
end

Wodarz1999_CTL_memory_response_HIV is "Wodarz1999 CTL memory response HIV"

Wodarz1999_CTL_memory_response_HIV model_entity_is "http://identifiers.org/biomodels.db/MODEL1006230062",
                                                   "http://identifiers.org/biomodels.db/BIOMD0000000683"
Wodarz1999_CTL_memory_response_HIV hypernym "http://identifiers.org/efo/0000764"
Wodarz1999_CTL_memory_response_HIV hypernym "http://identifiers.org/go/GO:0046718"
Wodarz1999_CTL_memory_response_HIV container "http://identifiers.org/bto/BTO:0002417"
Wodarz1999_CTL_memory_response_HIV taxon "http://identifiers.org/taxonomy/9606"
Wodarz1999_CTL_memory_response_HIV description "http://identifiers.org/pubmed/10588728"
