// Created by libAntimony v2.13.0
function Function_for_x_logistic_growth(phi_1, x, phi_2)
  phi_1*x*(1 - phi_2*x);
end

Function_for_x_logistic_growth is "Function for x logistic growth"

function Function_for_x_proliferation(delta, x, y, gamma_)
  delta*x*y/(gamma_ + x);
end

Function_for_x_proliferation is "Function for x proliferation"

function Function_for_x_immune_inactivation(nu_1, x, y)
  nu_1*x*y;
end

Function_for_x_immune_inactivation is "Function for x immune inactivation"

function Function_for_y_logistic_growth(sigma_1, y, sigma_2)
  sigma_1*y*(1 - sigma_2*y);
end

Function_for_y_logistic_growth is "Function for y logistic growth"

function Function_for_y_tumour_lysis(nu_2, x, y)
  nu_2*x*y;
end

Function_for_y_tumour_lysis is "Function for y tumour lysis"

function Function_for_u_production(nu_3, x, y)
  nu_3*x*y;
end

Function_for_u_production is "Function for u production"

function Function_for_u_decay(myu_1, u)
  myu_1*u;
end

Function_for_u_decay is "Function for u decay"

function Function_for_y__formation(x, y, rho)
  rho*x*y;
end

Function_for_y__formation is "Function for y* formation"

function Function_for_y__decay(myu_2, ystar)
  myu_2*ystar;
end

Function_for_y__decay is "Function for y* decay"


model *New_Model()

  // Compartments and Species:
  compartment compartment_;
  species x in compartment_, y in compartment_, u in compartment_, ystar in compartment_;

  // Rate Rules:
  R' = R*((sigma_1*y*(1 - sigma_2*y) - myu_2*ystar)/(y + ystar - 1))/3;

  // Reactions:
  x_logistic_growth:  => x; compartment_*Function_for_x_logistic_growth(phi_1, x, phi_2);
  x_proliferation:  => x; compartment_*Function_for_x_proliferation(delta, x, y, gamma_);
  x_immune_inactivation: x => ; compartment_*Function_for_x_immune_inactivation(nu_1, x, y);
  y_logistic_growth:  => y; compartment_*Function_for_y_logistic_growth(sigma_1, y, sigma_2);
  y_tumour_lysis: y => ; compartment_*Function_for_y_tumour_lysis(nu_2, x, y);
  u_production:  => u; compartment_*Function_for_u_production(nu_3, x, y);
  u_decay: u => ; compartment_*Function_for_u_decay(myu_1, u);
  ystar_formation:  => ystar; compartment_*Function_for_y__formation(x, y, rho);
  ystar_decay: ystar => ; compartment_*Function_for_y__decay(myu_2, ystar);

  // Species initializations:
  x = 0.3;
  y = 0.8;
  u = 1e-06;
  ystar = 0.1;

  // Compartment initializations:
  compartment_ = 1;

  // Variable initializations:
  R = 0.8;
  sigma_1 = 0.3;
  sigma_2 = 0.5;
  myu_2 = 0.24;
  phi_1 = 1.3398;
  phi_2 = 0.25;
  delta = 3.0218;
  nu_1 = 0.00218;
  nu_2 = 0.7279;
  nu_3 = 300;
  myu_1 = 1;
  rho = 0.1;
  gamma_ = 2.02;

  // Other declarations:
  var R;
  const compartment_, sigma_1, sigma_2, myu_2, phi_1, phi_2, delta, nu_1;
  const nu_2, nu_3, myu_1, rho, gamma_;

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

  // Display Names:
  compartment_ is "compartment";
  x is "Immune cell x";
  y is "Tumour cell y";
  u is "Chemokine concentration u";
  ystar is "Dead tumour cell ystar";
  gamma_ is "gamma";
  x_logistic_growth is "Immune cell x logistic growth";
  x_proliferation is "Immune cell x proliferation";
  x_immune_inactivation is "Immune cell x immune inactivation";
  y_logistic_growth is "Tumour cell y logistic growth";
  y_tumour_lysis is "Tumour cell y tumour lysis";
  u_production is "Chemokine concentration u production";
  u_decay is "Chemokine concentration u decay";
  ystar_formation is "Dead tumour cell ystar formation";
  ystar_decay is "Dead tumour cell ystar decay";

  // CV terms:
  compartment_ hypernym "http://identifiers.org/ncit/C13413"
  x hypernym "http://identifiers.org/ncit/C132890"
  y hypernym "http://identifiers.org/efo/0000311"
  u hypernym "http://identifiers.org/ncit/C20466"
  u hypernym "http://identifiers.org/ncit/C41185"
  ystar hypernym "http://identifiers.org/efo/0000311"
  ystar propertyBearer "http://identifiers.org/ncit/C28554"
  R hypernym "http://identifiers.org/efo/0000311"
  R hypernym "http://identifiers.org/ncit/C63921"
  nu_1 hypernym "http://identifiers.org/sbo/SBO:0000356"
  myu_1 hypernym "http://identifiers.org/sbo/SBO:0000356"
  gamma_ hypernym "http://identifiers.org/sbo/SBO:0000027"
  x_logistic_growth hypernym "http://identifiers.org/go/GO:0040007"
  x_logistic_growth hypernym "http://identifiers.org/sbo/SBO:0000393"
  x_proliferation hypernym "http://identifiers.org/sbo/SBO:0000393"
  x_immune_inactivation hypernym "http://identifiers.org/sbo/SBO:0000202"
  y_logistic_growth hypernym "http://identifiers.org/go/GO:0040007"
  y_logistic_growth hypernym "http://identifiers.org/sbo/SBO:0000393"
  y_tumour_lysis hypernym "http://identifiers.org/sbo/SBO:0000179"
  u_production hypernym "http://identifiers.org/sbo/SBO:0000393"
  u_decay hypernym "http://identifiers.org/sbo/SBO:0000179"
  ystar_formation hypernym "http://identifiers.org/go/SBO:0000393"
  ystar_decay hypernym "http://identifiers.org/sbo/SBO:0000179"
end

New_Model is "Malinzi2018 - tumour-immune interaction model"

New_Model model_entity_is "http://identifiers.org/biomodels.db/MODEL1909060001",
                          "http://identifiers.org/biomodels.db/BIOMD0000000809"
New_Model property "http://identifiers.org/go/GO:0002837"
New_Model property "http://identifiers.org/doid/DOID:162"
New_Model property "http://identifiers.org/efo/0000311"
New_Model property "http://identifiers.org/go/GO:0022611"
New_Model property "http://identifiers.org/mamo/MAMO_0000046"
New_Model description "http://identifiers.org/pubmed/30537482"
