// Created by libAntimony v2.13.0
function hydrolysis(kh, R)
  kh*R;
end

hydrolysis is "hydrolysis"

function sig_act(ke, r, kg, R, kf)
  ke*r/(1 + exp((kg - R)*kf));
end

sig_act is "Sigmoid Activation"

function hill_act(r, ke, R, h, kg)
  r*ke*R^h/(kg + R^h);
end

hill_act is "Hills activation"

function extraction(kminus1, r)
  kminus1*r;
end

extraction is "extraction"

function sig_act_t(r, ke, t, kg, R, kf)
  r*(ke*t/(100 + t))/(1 + exp((kg - R)*kf));
end

sig_act_t is "Sigmoid Activation 3 (t)"


model *Model_1()

  // Compartments and Species:
  compartment endosome;
  species r5 in endosome, R5 in endosome, r7 in endosome, R7 in endosome;

  // Reactions:
  reaction_0:  => r5; endosome*reaction_0_K1;
  reaction_1: r5 => R5; endosome*sig_act_t(r5, reaction_1_ke, time, reaction_1_kg, R5, reaction_1_kf);
  reaction_2: r5 => ; endosome*extraction(reaction_2_kminus1, r5);
  reaction_3:  => r7; endosome*reaction_3_K1;
  reaction_4: r7 => R7; endosome*hill_act(r7, reaction_4_ke, R7, reaction_4_h, reaction_4_kg);
  reaction_5: r7 => R7; endosome*sig_act(reaction_5_ke, r7, reaction_5_kg, R5, reaction_5_kf);
  reaction_6: R5 => r5; endosome*sig_act(reaction_6_ke, R5, reaction_6_kg, R7, reaction_6_kf);
  reaction_7: r7 => ; endosome*extraction(reaction_7_kminus1, r7);
  reaction_8: R5 => r5; endosome*hydrolysis(reaction_8_kh, R5);
  reaction_9: R7 => r7; endosome*hydrolysis(reaction_9_kh, R7);

  // Species initializations:
  r5 = 1;
  R5 = 0.001;
  r7 = 1;
  R7 = 0.001;

  // Compartment initializations:
  endosome = 1;

  // Variable initializations:
  reaction_0_K1 = 1;
  reaction_0_K1 has Mp;
  reaction_1_ke = 0.3;
  reaction_1_ke has ps;
  reaction_1_kg = 0.1;
  reaction_1_kg has M;
  reaction_1_kf = 2.5;
  reaction_1_kf has lpmole;
  reaction_2_kminus1 = 1;
  reaction_2_kminus1 has ps;
  reaction_3_K1 = 0.483;
  reaction_3_K1 has Mp;
  reaction_4_ke = 0.21;
  reaction_4_ke has ps;
  reaction_4_h = 3;
  reaction_4_h has dimensionless;
  reaction_4_kg = 0.1;
  reaction_5_ke = 0.021;
  reaction_5_ke has ps;
  reaction_5_kg = 1;
  reaction_5_kg has M;
  reaction_5_kf = 3;
  reaction_5_kf has lpmole;
  reaction_6_ke = 0.31;
  reaction_6_ke has ps;
  reaction_6_kg = 0.3;
  reaction_6_kg has M;
  reaction_6_kf = 3;
  reaction_6_kf has lpmole;
  reaction_7_kminus1 = 0.483;
  reaction_7_kminus1 has ps;
  reaction_8_kh = 0.06;
  reaction_8_kh has ps;
  reaction_9_kh = 0.15;
  reaction_9_kh has ps;

  // Other declarations:
  const endosome;

  // Unit definitions:
  unit time_unit = second;
  unit M = mole / litre;
  unit ps = 1 / second;
  unit Mp = mole / (second * litre);
  unit lpmole = litre / mole;

  // Display Names:
  time_unit is "sec";
  ps is "persec";
  Mp is "Mpers";
  lpmole is "lpermole";
  endosome is "endosomal membrane";
  r5 is "Rab5-GDP";
  R5 is "Rab5-GTP";
  r7 is "Rab7-GDP";
  R7 is "Rab7-GTP";
  reaction_0 is "recruitment of Rab5";
  reaction_1 is "activation of Rab5 (time)";
  reaction_2 is "extraction of Rab5";
  reaction_3 is "recruitment of Rab7";
  reaction_4 is "activation of Rab7 by GEF7";
  reaction_5 is "activation of Rab7 by GEF5";
  reaction_6 is "hydrolysis of Rab5 by Rab7";
  reaction_7 is "extraction of rab7";
  reaction_8 is "hydrolysis of Rab5 (intr.)";
  reaction_9 is "hydrolysis of Rab7 (intr.)";

  // CV terms:
  endosome identity "http://identifiers.org/go/GO:0010008"
  r5 part "http://identifiers.org/chebi/CHEBI:17552",
          "http://identifiers.org/uniprot/P20339"
  r5 identity "http://identifiers.org/go/GO:0031225"
  R5 part "http://identifiers.org/chebi/CHEBI:15996",
          "http://identifiers.org/uniprot/P20339"
  R5 identity "http://identifiers.org/go/GO:0031225"
  r7 part "http://identifiers.org/chebi/CHEBI:17552",
          "http://identifiers.org/uniprot/P51149"
  r7 identity "http://identifiers.org/go/GO:0031225"
  R7 part "http://identifiers.org/chebi/CHEBI:15996",
          "http://identifiers.org/uniprot/P51149"
  R7 identity "http://identifiers.org/go/GO:0031225"
  reaction_0 hypernym "http://identifiers.org/go/GO:0045184"
  reaction_1 hypernym "http://identifiers.org/go/GO:0032858"
  reaction_3 hypernym "http://identifiers.org/go/GO:0045184"
  reaction_4 hypernym "http://identifiers.org/go/GO:0017112",
                      "http://identifiers.org/go/GO:0032858"
  reaction_5 hypernym "http://identifiers.org/go/GO:0032858",
                      "http://identifiers.org/go/GO:0017112"
  reaction_6 hypernym "http://identifiers.org/go/GO:0003924",
                      "http://identifiers.org/go/GO:0005097"
  reaction_8 hypernym "http://identifiers.org/go/GO:0003924"
  reaction_9 hypernym "http://identifiers.org/go/GO:0003924"
end

Model_1 is "Del_Conte_Zerial2008_Rab5_Rab7_cut_out_switch"

Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL5937037510"
Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000174"
Model_1 description "http://identifiers.org/pubmed/18628746"
Model_1 origin "http://identifiers.org/pubmed/10591225",
               "http://identifiers.org/pubmed/16890441"
Model_1 hypernym "http://identifiers.org/go/GO:0032313"
Model_1 taxon "http://identifiers.org/taxonomy/9606"
Model_1 property "http://identifiers.org/mamo/MAMO_0000046"
