// Created by libAntimony v2.13.0
function function_for_normal_cell_growth_1(K, r_N)
  r_N/K;
end

function_for_normal_cell_growth_1 is "function for normal cell growth_1"

function function_for_cancer_cell_death_tissue_repair_system_1(K, beta_3, normalized_cancer_cell_a, normalized_normal_cell_n)
  beta_3*K*normalized_normal_cell_n*normalized_cancer_cell_a;
end

function_for_cancer_cell_death_tissue_repair_system_1 is "function for cancer cell death;tissue repair system_1"

function function_for_negative_effect_on_G_A_1(beta_5, normalized_cancer_cell_a, normalized_pre_cancer_cell_g)
  beta_5*normalized_cancer_cell_a*normalized_pre_cancer_cell_g;
end

function_for_negative_effect_on_G_A_1 is "function for negative effect on G;A_1"

function function_for_transition_to_cancer_cell_1(K, delta, normalized_pre_cancer_cell_g, xi)
  delta*normalized_pre_cancer_cell_g^2/(xi/K + normalized_pre_cancer_cell_g);
end

function_for_transition_to_cancer_cell_1 is "function for transition to cancer cell_1"

function function_for_normal_cell_damage_A_1(K, beta_1, normalized_cancer_cell_a, normalized_normal_cell_n)
  beta_1*K*normalized_normal_cell_n*normalized_cancer_cell_a;
end

function_for_normal_cell_damage_A_1 is "function for normal cell damage;A_1"

function function_for_negative_effect_on_A_G_1(beta_6, normalized_cancer_cell_a, normalized_pre_cancer_cell_g)
  beta_6*normalized_cancer_cell_a*normalized_pre_cancer_cell_g;
end

function_for_negative_effect_on_A_G_1 is "function for negative effect on A;G_1"

function function_for_normal_cell_damage_G_1(beta_4, normalized_normal_cell_n, normalized_pre_cancer_cell_g)
  beta_4*normalized_normal_cell_n*normalized_pre_cancer_cell_g;
end

function_for_normal_cell_damage_G_1 is "function for normal cell damage;G_1"

function function_for_pre_cancer_cell_logistic_growth_1(normalized_pre_cancer_cell_g, r_G)
  r_G*normalized_pre_cancer_cell_g;
end

function_for_pre_cancer_cell_logistic_growth_1 is "function for pre-cancer cell logistic growth_1"

function function_for_pre_cancer_cell_death_tissue_repair_system_1(K, beta_2, normalized_normal_cell_n, normalized_pre_cancer_cell_g)
  beta_2*K*normalized_normal_cell_n*normalized_pre_cancer_cell_g;
end

function_for_pre_cancer_cell_death_tissue_repair_system_1 is "function for pre-cancer cell death;tissue repair system_1"

function function_for_cancer_cell_logistic_growth_1(K, K_A, normalized_cancer_cell_a, r_A)
  r_A*normalized_cancer_cell_a*(1 - normalized_cancer_cell_a/(K_A/K));
end

function_for_cancer_cell_logistic_growth_1 is "function for cancer cell logistic growth_1"


model *New_Model()

  // Compartments and Species:
  compartment compartment_;
  species normalized_normal_cell_n in compartment_, normalized_pre_cancer_cell_g in compartment_;
  species normalized_cancer_cell_a in compartment_;

  // Assignment Rules:
  n0 := N0/K;
  g0 := G0/K;
  a0 := A0/K;
  A := normalized_cancer_cell_a*K;
  G := normalized_pre_cancer_cell_g*K;
  N := normalized_normal_cell_n*K;
  N0 := r_N/mu_N - 1;
  a := normalized_cancer_cell_a*10;

  // Reactions:
  normal_cell_growth:  => normalized_normal_cell_n; compartment_*function_for_normal_cell_growth_1(K, r_N);
  normal_cell_death: normalized_normal_cell_n => ; compartment_*mu_N*normalized_normal_cell_n;
  normal_cell_damage_A: normalized_normal_cell_n => ; compartment_*function_for_normal_cell_damage_A_1(K, beta_1, normalized_cancer_cell_a, normalized_normal_cell_n);
  normal_cell_damage_G: normalized_normal_cell_n => ; compartment_*function_for_normal_cell_damage_G_1(beta_4, normalized_normal_cell_n, normalized_pre_cancer_cell_g);
  pre_cancer_cell_logistic_growth:  => normalized_pre_cancer_cell_g; compartment_*function_for_pre_cancer_cell_logistic_growth_1(normalized_pre_cancer_cell_g, r_G);
  pre_cancer_cell_natural_death: normalized_pre_cancer_cell_g => ; compartment_*mu_G*normalized_pre_cancer_cell_g;
  pre_cancer_cell_death_tissue_repair_system: normalized_pre_cancer_cell_g => ; compartment_*function_for_pre_cancer_cell_death_tissue_repair_system_1(K, beta_2, normalized_normal_cell_n, normalized_pre_cancer_cell_g);
  pre_cancer_cell_death_apoptosis: normalized_pre_cancer_cell_g => ; compartment_*xi_G*normalized_pre_cancer_cell_g;
  negative_effect_on_G_A: normalized_pre_cancer_cell_g => ; compartment_*function_for_negative_effect_on_G_A_1(beta_5, normalized_cancer_cell_a, normalized_pre_cancer_cell_g);
  negative_effect_on_A_G: normalized_cancer_cell_a => ; compartment_*function_for_negative_effect_on_A_G_1(beta_6, normalized_cancer_cell_a, normalized_pre_cancer_cell_g);
  cancer_cell_natural_death: normalized_cancer_cell_a => ; compartment_*mu_A*normalized_cancer_cell_a;
  cancer_cell_logistic_growth:  => normalized_cancer_cell_a; compartment_*function_for_cancer_cell_logistic_growth_1(K, K_A, normalized_cancer_cell_a, r_A);
  cancer_cell_death_tissue_repair_system: normalized_cancer_cell_a => ; compartment_*function_for_cancer_cell_death_tissue_repair_system_1(K, beta_3, normalized_cancer_cell_a, normalized_normal_cell_n);
  cancer_cell_death_apoptosis: normalized_cancer_cell_a => ; compartment_*xi_A*normalized_cancer_cell_a;
  transition_to_cancer_cell: normalized_pre_cancer_cell_g => normalized_cancer_cell_a; compartment_*function_for_transition_to_cancer_cell_1(K, delta, normalized_pre_cancer_cell_g, xi);

  // Species initializations:
  normalized_normal_cell_n = n0;
  normalized_normal_cell_n has substance_per_volume;
  normalized_pre_cancer_cell_g = g0;
  normalized_pre_cancer_cell_g has substance_per_volume;
  normalized_cancer_cell_a = a0;
  normalized_cancer_cell_a has substance_per_volume;

  // Compartment initializations:
  compartment_ = 1;
  compartment_ has volume;

  // Variable initializations:
  r_N = 1000000;
  r_N has unit_2;
  mu_N = 0.01;
  mu_N has unit_2;
  beta_1 = 3.5e-10;
  beta_1 has unit_2;
  beta_4 = 0;
  beta_4 has unit_2;
  r_G = 0.05;
  r_G has unit_2;
  mu_G = 0.01;
  mu_G has unit_2;
  xi_G = 0.01;
  xi_G has unit_2;
  beta_2 = 3.5e-10;
  beta_2 has unit_2;
  beta_5 = 0;
  beta_5 has unit_2;
  delta = 1e-05;
  delta has unit_2;
  xi = 1000;
  xi has unit_1;
  r_A = 0.05;
  r_A has unit_2;
  K_A = 10000000;
  K_A has unit_1;
  mu_A = 0.01;
  mu_A has unit_2;
  xi_A = 0.006;
  xi_A has unit_2;
  beta_3 = 3.5e-10;
  beta_3 has unit_2;
  beta_6 = 0;
  beta_6 has unit_2;
  K = 100000000;
  G0 = 1;
  A0 = 0;

  // Other declarations:
  var n0, g0, a0, A, G, N, N0, a;
  const compartment_, r_N, mu_N, beta_1, beta_4, r_G, mu_G, xi_G, beta_2;
  const beta_5, delta, xi, r_A, K_A, mu_A, xi_A, beta_3, beta_6, K, G0, A0;

  // Unit definitions:
  unit length = metre;
  unit area = metre^2;
  unit volume = 1e-3 litre;
  unit time_unit = time_unit;
  unit substance = 1e-3 mole;
  unit unit_0 = 1 / 86400e-1 second;
  unit unit_1 = 1 / dimensionless^-0;
  unit unit_2 = 1 / 1e-3 second;
  unit extent = substance;
  unit substance_per_volume = 1e-3 mole / 1e-3 litre;

  // Display Names:
  time_unit is "time";
  unit_0 is "1/d";
  unit_1 is "1";
  unit_2 is "1/ms";
  compartment_ is "compartment";
  normalized_normal_cell_n is "normalized normal cell n";
  normalized_pre_cancer_cell_g is "normalized pre-cancer cell g";
  normalized_cancer_cell_a is "normalized cancer cell a";
  a is "a'";
  normal_cell_growth is "normal cell growth";
  normal_cell_death is "normal cell death";
  normal_cell_damage_A is "normal cell damage;A";
  normal_cell_damage_G is "normal cell damage;G";
  pre_cancer_cell_logistic_growth is "pre-cancer cell logistic growth";
  pre_cancer_cell_natural_death is "pre-cancer cell natural death";
  pre_cancer_cell_death_tissue_repair_system is "pre-cancer cell death;tissue repair system";
  pre_cancer_cell_death_apoptosis is "pre-cancer cell death;apoptosis";
  negative_effect_on_G_A is "negative effect on G;A";
  negative_effect_on_A_G is "negative effect on A;G";
  cancer_cell_natural_death is "cancer cell natural death";
  cancer_cell_logistic_growth is "cancer cell logistic growth";
  cancer_cell_death_tissue_repair_system is "cancer cell death;tissue repair system";
  cancer_cell_death_apoptosis is "cancer cell death;apoptosis";
  transition_to_cancer_cell is "transition to cancer cell";

  // CV terms:
  compartment_ hypernym "http://identifiers.org/ncit/C13413"
  normalized_normal_cell_n property "http://identifiers.org/ncit/C12508"
  normalized_normal_cell_n property "http://identifiers.org/ncit/C115935"
  n0 property "http://identifiers.org/ncit/C115935"
  n0 property "http://identifiers.org/ncit/C12508"
  normalized_pre_cancer_cell_g property "http://identifiers.org/ncit/C12959"
  normalized_pre_cancer_cell_g property "http://identifiers.org/ncit/C25629"
  g0 property "http://identifiers.org/ncit/C12959"
  g0 property "http://identifiers.org/ncit/C25629"
  normalized_cancer_cell_a property "http://identifiers.org/ncit/C12959"
  a0 property "http://identifiers.org/ncit/C12959"
  r_N property "http://identifiers.org/sbo/SBO:0000610"
  mu_N property "http://identifiers.org/ncit/C53346"
  mu_N property "http://identifiers.org/ncit/C85060"
  r_G property "http://identifiers.org/sbo/SBO:0000610"
  mu_G property "http://identifiers.org/ncit/C85060"
  mu_G property "http://identifiers.org/ncit/C53346"
  xi_G property "http://identifiers.org/ncit/C53346"
  delta property "http://identifiers.org/ncit/C25564"
  delta property "http://identifiers.org/go/GO:0000492"
  delta property "http://identifiers.org/ncit/C25636"
  xi property "http://identifiers.org/ncit/C48228"
  r_A property "http://identifiers.org/sbo/SBO:0000610"
  K_A property "http://identifiers.org/sbo/SBO:0000661"
  K_A property "http://identifiers.org/ncit/C81005"
  mu_A property "http://identifiers.org/ncit/C53346"
  mu_A property "http://identifiers.org/ncit/C85060"
  xi_A property "http://identifiers.org/ncit/C53346"
  A property "http://identifiers.org/ncit/C12959"
  G property "http://identifiers.org/ncit/C12959"
  G property "http://identifiers.org/ncit/C25629"
  N property "http://identifiers.org/ncit/C12508"
  N property "http://identifiers.org/ncit/C115935"
  G0 property "http://identifiers.org/ncit/C25629"
  G0 property "http://identifiers.org/ncit/C12959"
  A0 property "http://identifiers.org/ncit/C12959"
  N0 property "http://identifiers.org/ncit/C115935"
  N0 property "http://identifiers.org/ncit/C12508"
  a property "http://identifiers.org/ncit/C12959"
  normal_cell_growth property "http://identifiers.org/sbo/SBO:0000629"
  normal_cell_death property "http://identifiers.org/sbo/SBO:0000179"
  normal_cell_damage_A property "http://identifiers.org/sbo/SBO:0000202"
  normal_cell_damage_G property "http://identifiers.org/sbo/SBO:0000202"
  pre_cancer_cell_logistic_growth property "http://identifiers.org/go/GO:0040007"
  pre_cancer_cell_natural_death property "http://identifiers.org/sbo/SBO:0000179"
  pre_cancer_cell_death_tissue_repair_system property "http://identifiers.org/sbo/SBO:0000179"
  pre_cancer_cell_death_apoptosis property "http://identifiers.org/sbo/SBO:0000179"
  negative_effect_on_G_A property "http://identifiers.org/sbo/SBO:0000202"
  negative_effect_on_A_G property "http://identifiers.org/sbo/SBO:0000202"
  cancer_cell_natural_death property "http://identifiers.org/sbo/SBO:0000179"
  cancer_cell_logistic_growth property "http://identifiers.org/go/GO:0040007"
  cancer_cell_death_tissue_repair_system property "http://identifiers.org/sbo/SBO:0000179"
  cancer_cell_death_apoptosis property "http://identifiers.org/sbo/SBO:0000179"
  transition_to_cancer_cell property "http://identifiers.org/sbo/SBO:0000181"
end

New_Model is "Fassoni2019 - Oncogenesis encompassing mutations and genetic instability"

New_Model model_entity_is "http://identifiers.org/biomodels.db/MODEL1909050003",
                          "http://identifiers.org/biomodels.db/BIOMD0000000807"
New_Model property "http://identifiers.org/ncit/C18121"
New_Model property "http://identifiers.org/ncit/C19320"
New_Model property "http://identifiers.org/mamo/MAMO_0000046"
New_Model property "http://identifiers.org/ncit/C17938"
New_Model property "http://identifiers.org/ncit/C45576"
New_Model property "http://identifiers.org/ncit/C16870"
New_Model description "http://identifiers.org/pubmed/29947770"
