// Created by libAntimony v2.13.0
function function_2(v, E, R, T2, T1, k, S, h)
  v*exp((E/R)*(T2 - T1)/(T1*T2))/(k + S^h);
end

function_2 is "arhenius neg feedb tempvar"

function function_1(v, E, R, T2, T1, S)
  v*exp((E/R)*(T2 - T1)/(T1*T2))*S;
end

function_1 is "arhenius mass action tempvar"

function function_4(v, E, R, T2, T1, S)
  v*exp((E/R)*(T2 - T1)/(T1*T2))*S;
end

function_4 is "arhenius tranls temp var"

function function_3(v, E, R, T2, T1, S, Km)
  v*exp((E/R)*(T2 - T1)/(T1*T2))*S/(Km + S);
end

function_3 is "arhenius michaelis menten temp var"

function function_5(v, E, R, T2, T1, S1, S2, a)
  v*exp((E/R)*(T2 - T1)/(T1*T2))*S1*S2^a;
end

function_5 is "arhenius complexf temp var"


model *Model_1()

  // Compartments and Species:
  compartment default;
  species $s2 in default, s9 in default, s10 in default, s11 in default, $s13 in default;
  species species_1 in default, $species_2 in default, species_3 in default;
  species species_4 in default, species_12 in default;

  // Assignment Rules:
  T2 := 296 + (parameter_4/2)*sin(2*pi*time/parameter_5);
  parameter_6 := 50000;
  parameter_7 := 84000;

  // Reactions:
  re12: s10 => s11; default*function_1(re12_v, parameter_6, parameter_3, T2, T, s10);
  re13: $s2 => s9; default*function_2(re13_v, parameter_7, parameter_3, T2, T, re13_k, s11, re13_h);
  re14: s9 => species_12; default*function_3(re14_v, parameter_6, parameter_3, T2, T, s9, re14_Km);
  re15: s10 => species_12; default*function_3(re15_v, parameter_6, parameter_3, T2, T, s10, re15_Km);
  re16: s11 => species_12; default*function_3(re16_v, parameter_6, parameter_3, T2, T, s11, re16_Km);
  re18: $s13 => s10; default*function_4(re18_v, parameter_7, parameter_3, T2, T, s9);
  reaction_1: $species_2 => species_1; default*function_1(reaction_1_v, reaction_1_E, parameter_3, T2, T, species_2);
  reaction_2: species_3 + s11 => species_4; default*function_5(reaction_2_v, parameter_7, parameter_3, T2, T, species_3, s11, reaction_2_a);
  reaction_3: species_1 => species_3; default*function_1(parameter_1, parameter_9, parameter_3, T2, T, species_1);
  reaction_4: species_1 => species_12; default*function_3(reaction_4_v, reaction_4_E, parameter_3, T2, T, species_1, reaction_4_Km);
  reaction_5: species_4 => species_12; default*function_3(reaction_5_v, reaction_5_E, parameter_3, T2, T, species_4, reaction_5_Km);
  reaction_6: species_3 => species_1; default*function_1(parameter_2, parameter_10, parameter_3, T2, T, species_3);
  reaction_7: species_3 => species_12; default*function_3(parameter_8, reaction_7_E, parameter_3, T2, T, species_3, reaction_7_Km);

  // Species initializations:
  s2 = 1;
  s9 = 1;
  s10 = 1;
  s11 = 1;
  s13 = 1;
  species_1 = 1;
  species_2 = 1;
  species_3 = 1;
  species_4 = 1;
  species_12 = 1;

  // Compartment initializations:
  default = 1;

  // Variable initializations:
  T = 291;
  parameter_4 = 10;
  parameter_5 = 24;
  parameter_1 = 1;
  parameter_2 = 0.5;
  parameter_3 = 8.31447;
  parameter_8 = 1;
  parameter_9 = 60000;
  parameter_10 = 67000;
  re12_v = 0.1;
  re13_v = 2.6;
  re13_k = 0.4;
  re13_h = 2;
  re14_v = 3;
  re14_Km = 2;
  re15_v = 2.2;
  re15_Km = 0.2;
  re16_v = 1.5;
  re16_Km = 1.4;
  re18_v = 5;
  reaction_1_v = 19;
  reaction_1_E = 67000;
  reaction_2_v = 10;
  reaction_2_a = 2;
  reaction_4_v = 30;
  reaction_4_E = 67000;
  reaction_4_Km = 2;
  reaction_5_v = 20;
  reaction_5_E = 67000;
  reaction_5_Km = 4;
  reaction_7_E = 67000;
  reaction_7_Km = 1;

  // Other declarations:
  var T2, parameter_6, parameter_7;
  const default, T, parameter_4, parameter_5, parameter_1, parameter_2, parameter_3;
  const parameter_8, parameter_9, parameter_10;

  // Unit definitions:
  unit time_unit = 3600 second;
  unit substance = 1e-9 mole;

  // Display Names:
  time_unit is "time";
  s2 is "C3_Gene";
  s9 is "C3_mRNA";
  s10 is "C_3";
  s11 is "C_3_P";
  s13 is "C_3_pre";
  species_1 is "C1";
  species_2 is "C1_mRNA";
  species_3 is "C1_phos";
  species_4 is "c1c3complex";
  species_12 is "junk";
  parameter_4 is "amplitude";
  parameter_5 is "entrperiod";
  parameter_1 is "v_phos";
  parameter_2 is "V_dephos";
  parameter_3 is "R";
  parameter_6 is "EAlow";
  parameter_7 is "EAhigh";
  parameter_8 is "vphosdegr";
  parameter_9 is "Ephos";
  parameter_10 is "Edephos";
  re12 is "C3_phos";
  re13 is "C3_transk";
  re14 is "C3_mRNADegr";
  re15 is "C3_degr";
  re16 is "C3_phos_degr";
  re18 is "C3_transl";
  reaction_1 is "C1_transl";
  reaction_2 is "complexformation";
  reaction_3 is "C1_phos";
  reaction_4 is "C1_degr";
  reaction_5 is "complexdegr";
  reaction_6 is "C1_dephos";
  reaction_7 is "C1_phos_degr";

  // SBO terms:
  default.sboTerm = 290
  s2.sboTerm = 243
  s9.sboTerm = 278
  s10.sboTerm = 252
  s11.sboTerm = 252
  s13.sboTerm = 252
  species_1.sboTerm = 252
  species_2.sboTerm = 278
  species_3.sboTerm = 252
  species_4.sboTerm = 297
  species_12.sboTerm = 291
  T.sboTerm = 147
  re12.sboTerm = 216
  re13.sboTerm = 183
  re14.sboTerm = 179
  re15.sboTerm = 179
  re16.sboTerm = 179
  re18.sboTerm = 184
  reaction_1.sboTerm = 184
  reaction_2.sboTerm = 526
  reaction_3.sboTerm = 216
  reaction_4.sboTerm = 179
  reaction_5.sboTerm = 179
  reaction_6.sboTerm = 330
  reaction_7.sboTerm = 179

  // CV terms:
  default hypernym "http://identifiers.org/go/GO:0005623"
  s2 encodement "http://identifiers.org/uniprot/A8J6K7"
  s9 encodement "http://identifiers.org/uniprot/A8J6K7"
  s10 hypernym "http://identifiers.org/uniprot/A8J6K7"
  s11 hypernym "http://identifiers.org/uniprot/A8J6K7",
               "http://identifiers.org/kegg.compound/C00562"
  s13 hypernym "http://identifiers.org/uniprot/A8J6K7"
  species_1 hypernym "http://identifiers.org/uniprot/A8J2S3"
  species_2 encodement "http://identifiers.org/uniprot/A8J2S3"
  species_3 hypernym "http://identifiers.org/uniprot/A8J2S3",
                     "http://identifiers.org/kegg.compound/C00562"
  species_4 part "http://identifiers.org/uniprot/A8J6K7",
                 "http://identifiers.org/uniprot/A8J2S3"
  re12 hypernym "http://identifiers.org/go/GO:0016310"
  re13 hypernym "http://identifiers.org/go/GO:0009299"
  re14 hypernym "http://identifiers.org/go/GO:0006402"
  re15 hypernym "http://identifiers.org/go/GO:0030163"
  re16 hypernym "http://identifiers.org/go/GO:0030163"
  re18 hypernym "http://identifiers.org/go/GO:0006412"
  reaction_1 hypernym "http://identifiers.org/go/GO:0006412"
  reaction_2 hypernym "http://identifiers.org/go/GO:0006461"
  reaction_3 hypernym "http://identifiers.org/go/GO:0016310"
  reaction_4 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_5 hypernym "http://identifiers.org/go/GO:0030163"
  reaction_6 hypernym "http://identifiers.org/go/GO:0016311"
  reaction_7 hypernym "http://identifiers.org/go/GO:0030163"
end

Model_1 is "Heiland2012_CircadianClock_C.reinhardtii"

Model_1 model_entity_is "http://identifiers.org/biomodels.db/MODEL1201130000"
Model_1 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000411"
Model_1 description "http://identifiers.org/pubmed/23729908"
Model_1 taxon "http://identifiers.org/taxonomy/3055"
Model_1 hypernym "http://identifiers.org/go/GO:0060086"
