// Created by libAntimony v2.13.0
function function_1(v)
  v;
end

function_1 is "Constant flux (irreversible)"

function function_2(kcatPH, Ptot, O2, KdPH, Htot, HP)
  Htot*kcatPH*Ptot*O2/(1 + O2)/(KdPH + Ptot + HP);
end

function_2 is "vPH Htot"

function vFH(Ftot, O2, alpha, H, KiFH, HF, KcatFH)
  H*KcatFH*Ftot*O2/(alpha + O2)/(KiFH + Ftot + HF);
end

vFH is "vFH"

function vFA(Ftot, O2, alpha, A, gamma_, Atot, KiFA, KcatFH)
  A*KcatFH*Ftot*O2/(alpha + O2)/(KiFA + A + gamma_*(Atot - A));
end

vFA is "vFA"

function function_3(H, kcatPH, Ptot, O2, KdPH, HP)
  H*kcatPH*Ptot*O2/(1 + O2)/(KdPH + Ptot + HP);
end

function_3 is "vPH H"


model *Schmierer2010_FIH_Ankyrins()

  // Compartments and Species:
  compartment compartment_1;
  species species_1 in compartment_1, species_2 in compartment_1, species_3 in compartment_1;
  species $species_4 in compartment_1, $species_5 in compartment_1, $species_6 in compartment_1;
  species $species_7 in compartment_1, $species_8 in compartment_1, $species_9 in compartment_1;
  species $species_10 in compartment_1, $species_11 in compartment_1, $species_12 in compartment_1;
  species $species_13 in compartment_1, $species_14 in compartment_1, $species_15 in compartment_1;
  species $species_16 in compartment_1;

  // Assignment Rules:
  species_4 := species_1 - species_2;
  species_6 := species_5 - species_3;
  species_9 := 0.5*((species_2 - species_7 - parameter_7) + sqrt(((parameter_7 - species_2) + species_7)^2 + 4*species_2*parameter_7));
  parameter_7 := (parameter_2/parameter_3)*(parameter_3 + species_3 + parameter_6*(species_5 - species_3));
  species_10 := 0.5*((species_1 - species_8 - parameter_4) + sqrt(((parameter_4 - species_1) + species_8)^2 + 4*species_1*parameter_4));
  species_12 := (parameter_2 + species_9)/(parameter_7 + species_9);
  species_13 := species_2/(parameter_5 + species_1);
  species_14 := species_1/(parameter_5 + species_1);
  species_15 := (species_1 - species_2)/(parameter_5 + species_1);
  species_16 := species_3/species_5;
  parameter_14 := 1/parameter_11;
  parameter_16 := species_5/parameter_11;
  parameter_9 := (parameter_3/parameter_2)*(parameter_2 + species_9);
  parameter_13 := parameter_8*parameter_10;

  // Reactions:
  reaction_1:  => species_1; compartment_1*function_1(parameter_18);
  reaction_2: species_1 => ; compartment_1*parameter_17*species_1;
  reaction_3: species_1 => ; compartment_1*function_2(parameter_8, species_8, species_11, parameter_4, species_1, species_10);
  reaction_4:  => species_2; compartment_1*function_1(parameter_18);
  reaction_5: species_2 => ; compartment_1*parameter_17*species_2;
  reaction_6: species_2 => ; compartment_1*function_3(species_2, parameter_8, species_8, species_11, parameter_4, species_10);
  reaction_7: species_2 => ; compartment_1*vFH(species_7, species_11, parameter_1, species_2, parameter_7, species_9, parameter_13);
  reaction_8:  => species_3; compartment_1*function_1(parameter_16);
  reaction_9: species_3 => ; compartment_1*parameter_14*species_3;
  reaction_10: species_3 => ; compartment_1*vFA(species_7, species_11, parameter_1, species_3, parameter_6, species_5, parameter_9, parameter_13);

  // Species initializations:
  species_1 = 0;
  species_2 = 0;
  species_3 = 100;
  species_5 = 100;
  species_7 = 1;
  species_8 = 0.2;
  species_11 = 0;

  // Compartment initializations:
  compartment_1 = 1;
  parameter_7 has dimensionless;

  // Variable initializations:
  parameter_4 = 1;
  parameter_4 has dimensionless;
  parameter_2 = 1;
  parameter_2 has dimensionless;
  parameter_5 = 0.3;
  parameter_5 has dimensionless;
  parameter_1 = 0.33;
  parameter_1 has dimensionless;
  parameter_3 = 1;
  parameter_3 has dimensionless;
  parameter_6 = 0;
  parameter_6 has dimensionless;
  parameter_8 = 500;
  parameter_8 has dimensionless;
  parameter_10 = 1;
  parameter_10 has dimensionless;
  parameter_11 = 5;
  parameter_11 has dimensionless;
  parameter_14 has dimensionless;
  parameter_16 has dimensionless;
  parameter_9 has dimensionless;
  parameter_13 has dimensionless;
  parameter_17 = 1;
  parameter_17 has dimensionless;
  parameter_18 = 1;
  parameter_18 has dimensionless;

  // Other declarations:
  var parameter_7, parameter_14, parameter_16, parameter_9, parameter_13;
  const compartment_1, parameter_4, parameter_2, parameter_5, parameter_1;
  const parameter_3, parameter_6, parameter_8, parameter_10, parameter_11;
  const parameter_17, parameter_18;

  // Unit definitions:
  unit volume = dimensionless;
  unit time_unit = dimensionless;
  unit substance = dimensionless;

  // Display Names:
  compartment_1 is "Cell";
  species_1 is "Htot";
  species_2 is "H";
  species_3 is "A";
  species_4 is "HOH";
  species_5 is "Atot";
  species_6 is "AOH";
  species_7 is "Ftot";
  species_8 is "Ptot";
  species_9 is "HF";
  parameter_7 is "KiFH";
  species_10 is "HP";
  parameter_4 is "KdPH";
  species_11 is "O2";
  species_12 is "FIHfree";
  parameter_2 is "KdFH";
  species_13 is "CAD";
  parameter_5 is "KdHRE";
  species_14 is "NAD";
  species_15 is "CADOH";
  species_16 is "A for plotting";
  parameter_1 is "alpha";
  parameter_3 is "KdFA";
  parameter_6 is "gamma";
  parameter_8 is "kcatPH";
  parameter_10 is "w";
  parameter_11 is "eps";
  parameter_14 is "kdeg_A";
  parameter_16 is "ksyn_A";
  parameter_9 is "KiFA";
  parameter_13 is "kcatFH";
  parameter_17 is "kdeg_H";
  parameter_18 is "ksyn_H";
  reaction_1 is "Htot synthesis";
  reaction_2 is "Htot basal degradation";
  reaction_3 is "Htot induced degradation";
  reaction_4 is "H synthesis";
  reaction_5 is "H basal degardation";
  reaction_6 is "H induced degradation";
  reaction_7 is "H hydroxylation";
  reaction_8 is "A synthesis";
  reaction_9 is "A degradation";
  reaction_10 is "A hydroxylation";

  // SBO terms:
  compartment_1.sboTerm = 290
  species_1.sboTerm = 245
  species_2.sboTerm = 245
  species_3.sboTerm = 245
  species_4.sboTerm = 245
  species_5.sboTerm = 245
  species_6.sboTerm = 245
  species_7.sboTerm = 245
  species_8.sboTerm = 245
  species_9.sboTerm = 245
  parameter_7.sboTerm = 261
  species_10.sboTerm = 245
  parameter_4.sboTerm = 282
  species_11.sboTerm = 247
  species_12.sboTerm = 245
  parameter_2.sboTerm = 282
  species_13.sboTerm = 245
  parameter_5.sboTerm = 282
  species_14.sboTerm = 247
  species_15.sboTerm = 245
  parameter_1.sboTerm = 9
  parameter_3.sboTerm = 282
  parameter_6.sboTerm = 9
  parameter_8.sboTerm = 25
  parameter_10.sboTerm = 9
  parameter_11.sboTerm = 485
  parameter_14.sboTerm = 356
  parameter_16.sboTerm = 153
  parameter_9.sboTerm = 261
  parameter_13.sboTerm = 25
  parameter_17.sboTerm = 356
  parameter_18.sboTerm = 153
  reaction_1.sboTerm = 393
  reaction_2.sboTerm = 179
  reaction_3.sboTerm = 179
  reaction_4.sboTerm = 393
  reaction_5.sboTerm = 179
  reaction_6.sboTerm = 179
  reaction_7.sboTerm = 233
  reaction_8.sboTerm = 393
  reaction_9.sboTerm = 179
  reaction_10.sboTerm = 233

  // CV terms:
  compartment_1 hypernym "http://identifiers.org/go/GO:0005623"
  species_1 part "http://identifiers.org/uniprot/Q99814",
                 "http://identifiers.org/uniprot/Q16665",
                 "http://identifiers.org/uniprot/Q9Y2N7"
  species_2 hypernym "http://identifiers.org/uniprot/Q99814",
                     "http://identifiers.org/uniprot/Q16665",
                     "http://identifiers.org/uniprot/Q9Y2N7"
  species_3 hypernym "http://identifiers.org/uniprot/P16157"
  species_4 hypernym "http://identifiers.org/uniprot/Q16665",
                     "http://identifiers.org/uniprot/Q99814",
                     "http://identifiers.org/uniprot/Q9Y2N7"
  species_5 hypernym "http://identifiers.org/uniprot/P16157"
  species_6 hypernym "http://identifiers.org/uniprot/P16157"
  species_7 hypernym "http://identifiers.org/uniprot/Q9NWT6"
  species_8 hypernym "http://identifiers.org/uniprot/Q3T1B0",
                     "http://identifiers.org/uniprot/Q9NTU9"
  species_11 hypernym "http://identifiers.org/chebi/CHEBI:15379"
  reaction_1 hypernym "http://identifiers.org/go/GO:0009058"
  reaction_2 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_3 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_4 hypernym "http://identifiers.org/go/GO:0009058"
  reaction_5 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_6 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_7 hypernym "http://identifiers.org/go/GO:0018126"
  reaction_8 hypernym "http://identifiers.org/go/GO:0009058"
  reaction_9 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_10 hypernym "http://identifiers.org/go/GO:0018126"
end

Schmierer2010_FIH_Ankyrins is "Schmierer2010_FIH_Ankyrins"

Schmierer2010_FIH_Ankyrins model_entity_is "http://identifiers.org/biomodels.db/MODEL1008170000"
Schmierer2010_FIH_Ankyrins model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000300"
Schmierer2010_FIH_Ankyrins description "http://identifiers.org/pubmed/20955552"
Schmierer2010_FIH_Ankyrins taxon "http://identifiers.org/taxonomy/9606"
Schmierer2010_FIH_Ankyrins hypernym "http://identifiers.org/go/GO:0001666",
                                    "http://identifiers.org/go/GO:0070482"
Schmierer2010_FIH_Ankyrins property "http://identifiers.org/mamo/MAMO_0000046"
Schmierer2010_FIH_Ankyrins property "http://identifiers.org/doid/DOID:2835"
