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

Constant_flux__irreversible is "Constant flux (irreversible)"

function VD(Vm, X, Kx, S, Km, Den)
  (Vm/(1 + X/Kx))*S/Km/Den;
end

VD is "VD"

function V1_3_4_5(Vm, S, Km1, M, Km2)
  Vm*S/Km1/(1 + S/Km1 + M/Km2);
end

V1_3_4_5 is "V1,3,4,5"

function V2(Vm, S, Km)
  Vm*S/Km/(1 + S/Km);
end

V2 is "V2"


model *Ortega2013()

  // Compartments and Species:
  compartment Brain;
  species $APP in Brain, $C83 in Brain, $C99 in Brain, $AB in Brain, $X in Brain;
  species $p3 in Brain;

  // Assignment Rules:
  den := 1 + (C83/km3)*((1 + X/kiu1)/(1 + X/kic)) + (C99/km4)*((1 + X/kiu2)/(1 + X/kic));

  // Rate Rules:
  APP' = r0 - r1 - r2;
  C83' = r1 + r5 - r3__D;
  C99' = r2 - r5 - r4__D;
  AB' = r4__D;
  p3' = r3__D;

  // Reactions:
  r0:  => $APP; Brain*Constant_flux__irreversible(v0);
  r1: $APP => $C83; Brain*V1_3_4_5(vm1, APP, km1, C99, km5);
  r2: $APP => $C99; Brain*V2(vm2, APP, km2);
  r5: $C99 => $C83; Brain*V1_3_4_5(vm5, C99, km5, APP, km1);
  r3__D: $C83 => $p3; Brain*VD(vm3, X, kic, C83, km3, den);
  r4__D: $C99 => $AB; Brain*VD(vm4, X, kic, C99, km4, den);
  r3__ND: $C83 => $p3; Brain*V1_3_4_5(vm3, C83, km3, C99, km4);
  r4__ND: $C99 => $AB; Brain*V1_3_4_5(vm4, C99, km4, C83, km3);

  // Species initializations:
  APP = 0;
  C83 = 0;
  C99 = 0;
  AB = 0;
  X = 0;
  p3 = 0;

  // Compartment initializations:
  Brain = 1;

  // Variable initializations:
  v0 = 1;
  km1 = 0.186;
  vm1 = 1.1;
  km3 = 28.8;
  vm3 = 14.6;
  km4 = 0.915;
  vm4 = 1.71;
  km5 = 0.0672;
  vm5 = 0.0223;
  km2 = 1.64;
  vm2 = 0.153;
  kic = 0.173;
  kiu1 = 145;
  kiu2 = 7.31;

  // Other declarations:
  var den;
  const Brain, v0, km1, vm1, km3, vm3, km4, vm4, km5, vm5, km2, vm2, kic;
  const kiu1, kiu2;

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

  // Display Names:
  r3__D is "r3 (D)";
  r4__D is "r4 (D)";
  r3__ND is "r3 (ND)";
  r4__ND is "r4 (ND)";

  // CV terms:
  Brain identity "http://identifiers.org/bto/BTO:0000142"
  APP hypernym "http://identifiers.org/uniprot/P05067"
  C83 hypernym "http://identifiers.org/uniprot/P05067"
  C99 hypernym "http://identifiers.org/uniprot/P05067"
  AB hypernym "http://identifiers.org/uniprot/P05067"
  X identity "http://identifiers.org/chembl.compound/CHEMBL177969"
  p3 hypernym "http://identifiers.org/uniprot/P05067"
end

Ortega2013 is "Ortega2013 - Interplay between secretases determines biphasic amyloid-beta level"

Ortega2013 model_entity_is "http://identifiers.org/biomodels.db/MODEL1409240000"
Ortega2013 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000556"
Ortega2013 description "http://identifiers.org/pubmed/23152503"
Ortega2013 hypernym "http://identifiers.org/go/GO:0042987",
                    "http://identifiers.org/go/GO:0034205"
Ortega2013 property "http://identifiers.org/doid/DOID:10652"
Ortega2013 taxon "http://identifiers.org/taxonomy/9606"
