// Created by libAntimony v2.13.0
model *model_0000001()

  // Compartments and Species:
  compartment nucleus, cytoplasm;
  species M_T in cytoplasm, M_P in cytoplasm, T0 in cytoplasm, T1 in cytoplasm;
  species T2 in cytoplasm, P0 in cytoplasm, P1 in cytoplasm, P2 in cytoplasm;
  species C in cytoplasm, CN in nucleus, $Tt in cytoplasm, $Pt in cytoplasm;

  // Assignment Rules:
  Tt := T0 + T1 + T2 + C + CN*nucleus/cytoplasm;
  Pt := P0 + P1 + P2 + C + CN*nucleus/cytoplasm;
  v_dT := (1 + (v_dT_fac - 1)*ceil(sin((time/l_d)*pi)*0.9))*v_dT_dark;

  // Reactions:
  per_trans:  => M_P; per_trans_v_sP*per_trans_Ki_P^n/(per_trans_Ki_P^n + CN^n);
  tim_trans:  => M_T; tim_trans_v_sT*tim_trans_Ki_T^n/(tim_trans_Ki_T^n + CN^n);
  M_T_decay: M_T => ; (M_T_decay_v_mT/(M_T_decay_K_mT + M_T) + kd)*M_T*cytoplasm;
  M_P_decay: M_P => ; (M_P_decay_v_mP/(M_P_decay_K_mP + M_P) + kd)*M_P*cytoplasm;
  PER_transl:  => P0; PER_transl_k_sP*M_P*cytoplasm;
  TIM_transl:  => T0; TIM_transl_k_sT*M_T*cytoplasm;
  PO_decay: P0 => ; kd*P0*cytoplasm;
  P1_decay: P1 => ; kd*P1*cytoplasm;
  P2_decay: P2 => ; kd*P2*cytoplasm;
  T0_decay: T0 => ; kd*T0*cytoplasm;
  T1_decay: T1 => ; kd*T1*cytoplasm;
  T2_decay: T2 => ; kd*T2*cytoplasm;
  C_form: P2 + T2 => C; (C_form_k3*T2*P2 - C_form_k4*C)*cytoplasm;
  C_decay: C => ; C_decay_kd_C*C*cytoplasm;
  CN_decay: CN => ; CN_decay_kd_CN*CN*nucleus;
  C_transp: C -> CN; C_transp_k1*C*cytoplasm - C_transp_k2*CN*nucleus;
  P_pho: P0 => P1; (P_pho_V_1P*P0/(P_pho_K_1P + P0))*cytoplasm;
  P1_pho: P1 => P2; (P1_pho_V_3P*P1/(P1_pho_K_3P + P1))*cytoplasm;
  P1_depho: P1 => P0; (P1_depho_V_2P*P1/(P1_depho_K_2P + P1))*cytoplasm;
  P2_depho: P2 => P1; (P2_depho_V_4P*P2/(P2_depho_K_4P + P2))*cytoplasm;
  T_pho: T0 => T1; (T_pho_V_1T*T0/(T_pho_K_1T + T0))*cytoplasm;
  T1_pho: T1 => T2; (T1_pho_V_3T*T1/(T1_pho_K_3T + T1))*cytoplasm;
  T1_depho: T1 => T0; (T1_depho_V_2T*T1/(T1_depho_K_2T + T1))*cytoplasm;
  T2_depho: T2 => T1; (T2_depho_V_4T*T2/(T2_depho_K_4T + T2))*cytoplasm;
  T2_light_deact: T2 => ; (v_dT*T2/(T2_light_deact_K_dT + T2))*cytoplasm;
  P2_light_deact: P2 => ; (P2_light_deact_v_dP*P2/(P2_light_deact_K_dP + P2))*cytoplasm;

  // Species initializations:
  M_T = 1.41;
  M_P = 0.09;
  T0 = 0.54;
  T1 = 0.79;
  T2 = 4.65;
  P0 = 0.02;
  P1 = 0.02;
  P2 = 0.01;
  C = 0.18;
  CN = 1.2;

  // Compartment initializations:
  nucleus = 1;
  nucleus has litre;
  cytoplasm = 1;
  cytoplasm has litre;

  // Variable initializations:
  n = 4;
  n has dimensionless;
  kd = 0.01;
  kd has perh;
  v_dT has nMph;
  v_dT_fac = 2;
  v_dT_fac has dimensionless;
  l_d = 12;
  l_d has time_unit;
  v_dT_dark = 2;
  v_dT_dark has nMph;
  per_trans_v_sP = 0.8;
  per_trans_v_sP has nmph;
  per_trans_Ki_P = 1;
  per_trans_Ki_P has nM;
  tim_trans_v_sT = 1;
  tim_trans_v_sT has nmph;
  tim_trans_Ki_T = 1;
  tim_trans_Ki_T has nM;
  M_T_decay_v_mT = 0.7;
  M_T_decay_v_mT has nMph;
  M_T_decay_K_mT = 0.2;
  M_T_decay_K_mT has nM;
  M_P_decay_v_mP = 0.8;
  M_P_decay_v_mP has nMph;
  M_P_decay_K_mP = 0.2;
  M_P_decay_K_mP has nM;
  PER_transl_k_sP = 0.9;
  PER_transl_k_sP has perh;
  TIM_transl_k_sT = 0.9;
  TIM_transl_k_sT has perh;
  C_form_k3 = 1.2;
  C_form_k3 has pnMph;
  C_form_k4 = 0.6;
  C_form_k4 has perh;
  C_decay_kd_C = 0.01;
  C_decay_kd_C has perh;
  CN_decay_kd_CN = 0.01;
  CN_decay_kd_CN has perh;
  C_transp_k1 = 1.2;
  C_transp_k1 has perh;
  C_transp_k2 = 0.2;
  C_transp_k2 has perh;
  P_pho_V_1P = 8;
  P_pho_V_1P has nMph;
  P_pho_K_1P = 2;
  P_pho_K_1P has nM;
  P1_pho_V_3P = 8;
  P1_pho_V_3P has nMph;
  P1_pho_K_3P = 2;
  P1_pho_K_3P has nM;
  P1_depho_K_2P = 2;
  P1_depho_K_2P has nM;
  P1_depho_V_2P = 1;
  P1_depho_V_2P has nMph;
  P2_depho_V_4P = 1;
  P2_depho_V_4P has nMph;
  P2_depho_K_4P = 2;
  P2_depho_K_4P has nM;
  T_pho_V_1T = 8;
  T_pho_V_1T has nMph;
  T_pho_K_1T = 2;
  T_pho_K_1T has nM;
  T1_pho_V_3T = 8;
  T1_pho_V_3T has nMph;
  T1_pho_K_3T = 2;
  T1_pho_K_3T has nM;
  T1_depho_K_2T = 2;
  T1_depho_K_2T has nM;
  T1_depho_V_2T = 1;
  T1_depho_V_2T has nMph;
  T2_depho_V_4T = 1;
  T2_depho_V_4T has nMph;
  T2_depho_K_4T = 2;
  T2_depho_K_4T has nM;
  T2_light_deact_K_dT = 0.2;
  T2_light_deact_K_dT has nM;
  P2_light_deact_v_dP = 2;
  P2_light_deact_v_dP has nMph;
  P2_light_deact_K_dP = 0.2;
  P2_light_deact_K_dP has nM;

  // Other declarations:
  var v_dT;
  const nucleus, cytoplasm, n, kd, v_dT_fac, l_d, v_dT_dark;

  // Unit definitions:
  unit substance = 1e-9 mole;
  unit nM = 1e-9 mole / litre;
  unit time_unit = 3.6e3 second;
  unit nMph = 1e-9 mole / (3.6e3 second * litre);
  unit perh = 1 / 3.6e3 second;
  unit pnMph = litre / (3.6e3 second * 1e-9 mole);
  unit nmph = 1e-9 mole / 3.6e3 second;

  // Display Names:
  substance is "nanomolar";
  nM is "nanomoleperlitre";
  time_unit is "hours";
  nMph is "nanoMperHour";
  perh is "perhour";
  pnMph is "pernMperHour";
  nmph is "nanomolperhour";
  M_T is "tim mRNA";
  M_P is "per mRNA";
  T0 is "TIM";
  T1 is "TIM-p";
  T2 is "TIM-pp";
  P0 is "PER";
  P1 is "PER-p";
  P2 is "PER-pp";
  C is "PER_TIM complex cytoplasm";
  CN is "PER_TIM complex nuclear";
  Tt is "total TIM";
  Pt is "total PER";
  n is "transkr_rep_hill_coefficient";
  kd is "degradation_rate";
  v_dT is "T2_lightdecay_rate";
  v_dT_fac is "v_dT_fold_incr_during_light";
  l_d is "light_dark_period";
  v_dT_dark is "v_dT_value_darkness";
  per_trans is "per transkription";
  tim_trans is "tim transkription";
  M_T_decay is "tim mRNA decay";
  M_P_decay is "per mRNA decay";
  PER_transl is "PER tranlation";
  TIM_transl is "TIM translation";
  PO_decay is "PER decay";
  P1_decay is "PER-p decay";
  P2_decay is "PER-pp decay";
  T0_decay is "TIM decay";
  T1_decay is "TIM-p decay";
  T2_decay is "TIM-pp decay";
  C_form is "Per_TIM complex formation";
  C_decay is "cytopl. PER_TIM compl. decay";
  CN_decay is "nuclear PER_TIM compl. decay";
  C_transp is "PER_TIM complex shuttling";
  P_pho is "PER phosphorylation";
  P1_pho is "PER-p phosphorylation";
  P1_depho is "PER-p dephosphorylation";
  P2_depho is "PER-pp dephosphorylation";
  T_pho is "TIM phosphorylation";
  T1_pho is "TIM-p phosphorylation";
  T1_depho is "TIM-p dephosphorylation";
  T2_depho is "TIM-pp dephosphorylation";
  T2_light_deact is "TIM-pp light deactivation";
  P2_light_deact is "PER-pp light deactivation";

  // CV terms:
  nucleus identity "http://identifiers.org/go/GO:0005634"
  cytoplasm identity "http://identifiers.org/go/GO:0005737"
  M_T hypernym "http://identifiers.org/chebi/CHEBI:33699",
               "http://identifiers.org/kegg.compound/C02100"
  M_P hypernym "http://identifiers.org/chebi/CHEBI:33699",
               "http://identifiers.org/kegg.compound/C02100"
  T0 hypernym "http://identifiers.org/uniprot/P49021"
  T1 hypernym "http://identifiers.org/uniprot/P49021",
              "http://identifiers.org/kegg.compound/C00562"
  T2 hypernym "http://identifiers.org/uniprot/P49021"
  P0 hypernym "http://identifiers.org/uniprot/P07663"
  P1 hypernym "http://identifiers.org/uniprot/P07663",
              "http://identifiers.org/kegg.compound/C00562"
  P2 hypernym "http://identifiers.org/uniprot/P07663",
              "http://identifiers.org/kegg.compound/C00562"
  C part "http://identifiers.org/uniprot/P07663",
         "http://identifiers.org/uniprot/P49021"
  C hypernym "http://identifiers.org/go/GO:0043234"
  CN part "http://identifiers.org/uniprot/P07663",
          "http://identifiers.org/uniprot/P49021"
  CN hypernym "http://identifiers.org/go/GO:0043234"
  Tt version "http://identifiers.org/uniprot/P49021"
  Pt version "http://identifiers.org/uniprot/P07663"
  per_trans hypernym "http://identifiers.org/go/GO:0009299"
  tim_trans identity "http://identifiers.org/go/GO:0009299"
  M_T_decay hypernym "http://identifiers.org/go/GO:0006402"
  M_P_decay hypernym "http://identifiers.org/go/GO:0006402"
  PER_transl hypernym "http://identifiers.org/go/GO:0006412"
  TIM_transl hypernym "http://identifiers.org/go/GO:0006412"
  PO_decay hypernym "http://identifiers.org/go/GO:0030163"
  P1_decay hypernym "http://identifiers.org/go/GO:0030163"
  P2_decay hypernym "http://identifiers.org/go/GO:0030163"
  T0_decay hypernym "http://identifiers.org/go/GO:0030163"
  T1_decay hypernym "http://identifiers.org/go/GO:0030163"
  T2_decay hypernym "http://identifiers.org/go/GO:0030163"
  C_form part "http://identifiers.org/go/GO:0043241",
              "http://identifiers.org/go/GO:0006461"
  C_decay hypernym "http://identifiers.org/go/GO:0030163"
  CN_decay hypernym "http://identifiers.org/go/GO:0030163"
  C_transp part "http://identifiers.org/go/GO:0006606",
                "http://identifiers.org/go/GO:0006611"
  C_transp hypernym "http://identifiers.org/go/GO:0006886"
  P_pho hypernym "http://identifiers.org/ec-code/2.7.11.1",
                 "http://identifiers.org/kegg.reaction/R00162",
                 "http://identifiers.org/go/GO:0006468"
  P1_pho hypernym "http://identifiers.org/ec-code/2.7.11.1",
                  "http://identifiers.org/kegg.reaction/R00162",
                  "http://identifiers.org/go/GO:0006468"
  P1_depho hypernym "http://identifiers.org/ec-code/3.1.3.16",
                    "http://identifiers.org/go/GO:0006470"
  P2_depho hypernym "http://identifiers.org/ec-code/3.1.3.16",
                    "http://identifiers.org/go/GO:0006470"
  T_pho hypernym "http://identifiers.org/ec-code/2.7.11.1",
                 "http://identifiers.org/kegg.reaction/R00162",
                 "http://identifiers.org/go/GO:0006468"
  T1_pho hypernym "http://identifiers.org/ec-code/2.7.11.1",
                  "http://identifiers.org/kegg.reaction/R00162",
                  "http://identifiers.org/go/GO:0006468"
  T1_depho hypernym "http://identifiers.org/ec-code/3.1.3.16",
                    "http://identifiers.org/go/GO:0006470"
  T2_depho hypernym "http://identifiers.org/ec-code/3.1.3.16",
                    "http://identifiers.org/go/GO:0006470"
  T2_light_deact hypernym "http://identifiers.org/go/GO:0030163"
  P2_light_deact hypernym "http://identifiers.org/go/GO:0030163"
end

model_0000001 is "Leloup1998_CircClock_LD"

model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL0243843132"
model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000171"
model_0000001 description "http://identifiers.org/pubmed/9486845"
model_0000001 origin "http://identifiers.org/biomodels.db/BIOMD0000000016"
model_0000001 taxon "http://identifiers.org/taxonomy/7227"
model_0000001 parthood "http://identifiers.org/kegg.pathway/dme04710"
model_0000001 hypernym "http://identifiers.org/go/GO:0042752"
