// Created by libAntimony v2.13.0
model *YeastWTmodel2()

  // Compartments and Species:
  compartment cellMembrane, nucleus;
  substanceOnly species Ctelo in nucleus, Utelo in nucleus, Cdc13 in nucleus;
  substanceOnly species Rad17Utelo in nucleus, Rad17 in nucleus, Rad24 in nucleus;
  substanceOnly species RPA in nucleus, Mec1 in nucleus, ssDNA in nucleus;
  substanceOnly species RPAssDNA in nucleus, RPAssDNA1 in nucleus, RPAssDNA2 in nucleus;
  substanceOnly species Mec1RPAssDNA in nucleus, ExoXI in nucleus, ExoXA in nucleus;
  substanceOnly species Exo1I in nucleus, Exo1A in nucleus, Rad9I in nucleus;
  substanceOnly species Rad9A in nucleus, Rad53I in nucleus, Rad53A in nucleus;
  substanceOnly species Chk1I in nucleus, Chk1A in nucleus, Dun1I in nucleus;
  substanceOnly species Dun1A in nucleus, ATP in nucleus, ADP in nucleus;
  substanceOnly species Rad9Kin in nucleus, recovery in nucleus, G1 in nucleus;
  substanceOnly species S in nucleus, G2 in nucleus, M in nucleus, G1cyclin in nucleus;
  substanceOnly species Scyclin in nucleus, G2cyclin in nucleus, Mcyclin in nucleus;
  substanceOnly species G1CdkI in nucleus, G1CdkA in nucleus, SCdkI in nucleus;
  substanceOnly species SCdkA in nucleus, G2CdkI in nucleus, G2CdkA in nucleus;
  substanceOnly species MCdkI in nucleus, MCdkA in nucleus, G1Soff in nucleus;
  substanceOnly species G1Son in nucleus, SG2off in nucleus, SG2on in nucleus;
  substanceOnly species G2Moff in nucleus, G2Mon in nucleus, MG1off in nucleus;
  substanceOnly species MG1on in nucleus, $sink in nucleus, budscar in cellMembrane;

  // Reactions:
  Capping: Cdc13 + Utelo => Ctelo; Capping_k1*Cdc13*Utelo*kalive;
  Uncapping: Ctelo => Cdc13 + Utelo; Uncapping_k2*Ctelo*kalive;
  Rad17binding: Utelo + Rad17 + Rad24 + ATP => Rad17Utelo + Rad24 + ADP; Rad17binding_k3*Utelo*Rad17*Rad24*ATP*kalive/(5000 + ATP);
  ExoXactivation: ExoXI + Rad17Utelo => ExoXA + Rad17Utelo; ExoXactivation_k4*ExoXI*Rad17Utelo*kalive;
  ExoXactivity: ExoXA + Rad17Utelo => ExoXA + Rad17Utelo + ssDNA; ExoXactivity_k5*ExoXA*Rad17Utelo*kalive;
  Exo1activation: Exo1I => Exo1A; Exo1activation_k6a*Exo1I*kalive;
  Exo1Rad24dependentActivation: Exo1I + Rad24 => Exo1A + Rad24; Exo1Rad24dependentActivation_k6b*Exo1I*Rad24*kalive;
  Exo1Rad17independentActivity: Utelo + Exo1A => Utelo + Exo1A + ssDNA; Exo1Rad17independentActivity_k7a*Utelo*Exo1A*kalive;
  Exo1Rad17dependentActivity: Rad17Utelo + Exo1A => Rad17Utelo + Exo1A + ssDNA; Exo1Rad17dependentActivity_k7b*Rad17Utelo*Exo1A*kalive;
  RPAbinding1: ssDNA + RPA => RPAssDNA1; RPAbinding1_k8a*RPA*ssDNA*kalive;
  RPAbinding2: ssDNA + RPAssDNA1 => RPAssDNA2; RPAbinding2_k8b*RPAssDNA1*ssDNA*kalive;
  RPAbinding: ssDNA + RPAssDNA2 => RPAssDNA; RPAbinding_k8c*RPAssDNA2*ssDNA*kalive;
  Mec1binding: RPAssDNA + Mec1 => Mec1RPAssDNA; Mec1binding_k8d*RPAssDNA*Mec1*kalive;
  Rad9activation: Rad9Kin + Rad9I => Rad9Kin + Rad9A; Rad9activation_k9*Rad9Kin*Rad9I*kalive;
  ExoXinhibition: ExoXA + Rad9A => ExoXI + Rad9A; ExoXA*ExoXinhibition_k10a*Rad9A*kalive;
  ExoXinhibition2: ExoXA + Rad9I => ExoXI + Rad9I; ExoXA*ExoXinhibition2_k10b*Rad9I*kalive;
  Rad53activation: Rad53I + Rad9A => Rad53A + Rad9A; Rad53activation_k11*Rad53I*Rad9A*kalive;
  Chk1Activation: Chk1I + Rad9A => Chk1A + Rad9A; Chk1I*Chk1Activation_k12*Rad9A*kalive;
  Exo1inhibition: Exo1A + Rad53A => Exo1I + Rad53A; Exo1A*Exo1inhibition_k13*Rad53A*kalive;
  Dun1activation: Dun1I + Rad53A => Dun1A + Rad53A; Dun1I*Dun1activation_k14*Rad53A*kalive;
  Chk1cellArrest: Chk1A + G2Mon => Chk1A + G2Moff; Chk1A*G2Mon*Chk1cellArrest_k15*kalive;
  Dun1cellArrest: Dun1A + G2Mon => Dun1A + G2Moff; Dun1A*G2Mon*Dun1cellArrest_k16*kalive;
  SDNArepair1: Mec1RPAssDNA + S => Mec1 + RPA + S + 3 ssDNA; SDNArepair1_k17a*Mec1RPAssDNA*S*kalive;
  G2DNArepair1: G2 + G2Moff + Mec1RPAssDNA => G2 + G2Moff + Mec1 + RPA + 3 ssDNA; G2*G2Moff*G2DNArepair1_k17b*Mec1RPAssDNA*kalive;
  SDNArepair2: S + ssDNA => S; SDNArepair2_k18a*S*ssDNA*kalive;
  G2DNArepair2: G2 + G2Moff + ssDNA => G2 + G2Moff; G2*G2Moff*G2DNArepair2_k18b*ssDNA*kalive;
  Recovery: Cdc13 + Rad17Utelo + recovery => Ctelo + Rad17 + recovery; Cdc13*Recovery_k19*Rad17Utelo*recovery*kalive;
  G1cyclinSynthesis: G1 => G1cyclin + G1; G1*G1cyclinSynthesis_kc1*kalive;
  ScyclinSynthesis: S => Scyclin + S; ScyclinSynthesis_kc1*S*kalive;
  G2cyclinSynthesis: G2 => G2cyclin + G2; G2*G2cyclinSynthesis_kc1*kalive;
  McyclinSynthesis: M => Mcyclin + M; McyclinSynthesis_kc1*M*kalive;
  G1toSGenesOn: G1Soff + G1 + G1CdkA => G1Son + G1 + G1CdkA; G1*G1CdkA*G1Soff*G1toSGenesOn_kc2*kalive;
  StoG2GenesOn: SG2off + S + SCdkA => SG2on + S + SCdkA; StoG2GenesOn_kc2*S*SCdkA*SG2off*kalive;
  G2toMGenesOn: G2Moff + G2 + G2CdkA => G2Mon + G2 + G2CdkA; G2*G2CdkA*G2Moff*G2toMGenesOn_kc2*kalive;
  MtoG1GenesOn: MG1off + M + MCdkA => MG1on + M + MCdkA; MtoG1GenesOn_kc2*M*MCdkA*MG1off*kalive;
  G1cyclinDegradation: G1cyclin => $sink; G1cyclin*G1cyclinDegradation_kc3*kalive;
  ScyclinDegradation: Scyclin => $sink; ScyclinDegradation_kc3*Scyclin*kalive;
  G2cyclinDegradation: G2cyclin => $sink; G2cyclin*G2cyclinDegradation_kc3*kalive;
  McyclinDegradation: Mcyclin => $sink; McyclinDegradation_kc3*Mcyclin*kalive;
  G1toSProgession: G1 + G1CdkA + G1Son => G1CdkI + G1Soff + S; G1*G1CdkA*G1Son*G1toSProgession_kc4*kalive;
  StoG2Progession: S + SCdkA + SG2on => G2 + SCdkI + SG2off; StoG2Progession_kc4*S*SCdkA*SG2on*kalive;
  G2toMProgession: G2 + G2CdkA + G2Mon => G2CdkI + G2Moff + M; G2*G2CdkA*G2Mon*G2toMProgession_kc4*kalive;
  MtoG1Progession: M + MCdkA + MG1on => budscar + G1 + MCdkI + MG1off; MtoG1Progession_kc4*M*MCdkA*MG1on*kalive;

  // Events:
  Rad9KinaseActivation: at Mec1RPAssDNA >= 800: Rad9Kin = 1;
  ssDNAremoval: at (Mec1RPAssDNA + RPAssDNA + ssDNA) <= 1: ssDNA = 0, RPAssDNA = 0, Mec1RPAssDNA = 0, recovery = 1;
  G2MRecoveryCompleted: at (G2 == 1) && (Rad17Utelo == 0): Rad53A = 0, Rad53I = 6900, ExoXI = 70, ExoXA = 0, Exo1I = 670, Exo1A = 0, Dun1I = 3000, Dun1A = 0, Chk1I = 60, Chk1A = 0, Rad9I = 20, Rad9A = 0, recovery = 0, G2Moff = 0, G2Mon = 1;
  SphaseRecoveryCompleted: at Rad17Utelo == 0: recovery = 0;
  G1CdkActivation: at G1cyclin > 100: G1CdkI = 0, G1CdkA = 1;
  SCdkActivation: at Scyclin > 100: SCdkI = 0, SCdkA = 1;
  G2CdkActivation: at G2cyclin > 100: G2CdkI = 0, G2CdkA = 1;
  MCdkActivation: at Mcyclin > 100: MCdkI = 0, MCdkA = 1;
  CellDeath: at (Mec1RPAssDNA + RPAssDNA + ssDNA) >= 2000: kalive = 0;

  // Species initializations:
  Ctelo = 64/nucleus;
  Utelo = 0;
  Cdc13 = 300/nucleus;
  Rad17Utelo = 0;
  Rad17 = 70/nucleus;
  Rad24 = 70/nucleus;
  RPA = 4000/nucleus;
  Mec1 = 4000/nucleus;
  ssDNA = 0;
  RPAssDNA = 0;
  RPAssDNA1 = 0;
  RPAssDNA2 = 0;
  Mec1RPAssDNA = 0;
  ExoXI = 70/nucleus;
  ExoXA = 0;
  Exo1I = 670/nucleus;
  Exo1A = 0;
  Rad9I = 20/nucleus;
  Rad9A = 0;
  Rad53I = 6900/nucleus;
  Rad53A = 0;
  Chk1I = 60/nucleus;
  Chk1A = 0;
  Dun1I = 3000/nucleus;
  Dun1A = 0;
  ATP = 10000/nucleus;
  ADP = 1000/nucleus;
  Rad9Kin = 0;
  recovery = 0;
  G1 = 1/nucleus;
  S = 0;
  G2 = 0;
  M = 0;
  G1cyclin = 0;
  Scyclin = 0;
  G2cyclin = 0;
  Mcyclin = 0;
  G1CdkI = 1/nucleus;
  G1CdkA = 0;
  SCdkI = 1/nucleus;
  SCdkA = 0;
  G2CdkI = 1/nucleus;
  G2CdkA = 0;
  MCdkI = 1/nucleus;
  MCdkA = 0;
  G1Soff = 1/nucleus;
  G1Son = 0;
  SG2off = 1/nucleus;
  SG2on = 0;
  G2Moff = 1/nucleus;
  G2Mon = 0;
  MG1off = 1/nucleus;
  MG1on = 0;
  sink = 0;
  budscar = 0;

  // Compartment initializations:
  cellMembrane = 1;
  nucleus = 1;

  // Variable initializations:
  kalive = 1;
  Capping_k1 = 0.0005;
  Uncapping_k2 = 0.000385;
  Rad17binding_k3 = 1.5e-08;
  ExoXactivation_k4 = 0.01;
  ExoXactivity_k5 = 0.0003;
  Exo1activation_k6a = 5e-05;
  Exo1Rad24dependentActivation_k6b = 0.0005;
  Exo1Rad17independentActivity_k7a = 3e-05;
  Exo1Rad17dependentActivity_k7b = 3e-05;
  RPAbinding1_k8a = 0.001;
  RPAbinding2_k8b = 100;
  RPAbinding_k8c = 100;
  Mec1binding_k8d = 0.004;
  Rad9activation_k9 = 100;
  ExoXinhibition_k10a = 0.05;
  ExoXinhibition2_k10b = 0.05;
  Rad53activation_k11 = 1e-05;
  Chk1Activation_k12 = 0.00017;
  Exo1inhibition_k13 = 1;
  Dun1activation_k14 = 3.3e-06;
  Chk1cellArrest_k15 = 0.2;
  Dun1cellArrest_k16 = 0.1;
  SDNArepair1_k17a = 0.05;
  G2DNArepair1_k17b = 0.05;
  SDNArepair2_k18a = 0.001;
  G2DNArepair2_k18b = 1e-05;
  Recovery_k19 = 0.001;
  G1cyclinSynthesis_kc1 = 0.16;
  ScyclinSynthesis_kc1 = 0.16;
  G2cyclinSynthesis_kc1 = 0.16;
  McyclinSynthesis_kc1 = 0.16;
  G1toSGenesOn_kc2 = 0.01;
  StoG2GenesOn_kc2 = 0.01;
  G2toMGenesOn_kc2 = 0.01;
  MtoG1GenesOn_kc2 = 0.01;
  G1cyclinDegradation_kc3 = 0.0012;
  ScyclinDegradation_kc3 = 0.0012;
  G2cyclinDegradation_kc3 = 0.0012;
  McyclinDegradation_kc3 = 0.0012;
  G1toSProgession_kc4 = 0.01;
  StoG2Progession_kc4 = 0.01;
  G2toMProgession_kc4 = 0.01;
  MtoG1Progession_kc4 = 0.01;

  // Other declarations:
  var kalive;
  const cellMembrane, nucleus;

  // Unit definitions:
  unit substance = item;

  // Display Names:
  Exo1activation is "Rad24independentExo1Activation";
  Exo1Rad24dependentActivation is "Rad24dependentExo1Activation";
  Exo1Rad17independentActivity is "Rad17independentExo1Activity";
  Exo1Rad17dependentActivity is "Rad17dependentExo1Activity";
  RPAbinding1 is "RPAbinding-stage1";
  RPAbinding2 is "RPAbinding-stage2";
  RPAbinding is "RPAbinding-completed";

  // CV terms:
  cellMembrane hypernym "http://identifiers.org/obo.go/GO:0016020"
  nucleus hypernym "http://identifiers.org/obo.go/GO:0005634"
  Ctelo part "http://identifiers.org/obo.go/GO:0000782"
  Ctelo hypernym "http://identifiers.org/obo.go/GO:0000781"
  Utelo hypernym "http://identifiers.org/obo.go/GO:0000781"
  Cdc13 identity "http://identifiers.org/uniprot/P32797"
  Rad17Utelo part "http://identifiers.org/uniprot/P48581",
                  "http://identifiers.org/obo.go/GO:0000781"
  Rad17 identity "http://identifiers.org/uniprot/P48581"
  Rad24 identity "http://identifiers.org/uniprot/P32641"
  RPA hypernym "http://identifiers.org/pirsf/PIRSF002091"
  Mec1 identity "http://identifiers.org/uniprot/P38111"
  ssDNA hypernym "http://identifiers.org/obo.chebi/CHEBI:09160",
                 "http://identifiers.org/kegg.compound/C00271"
  RPAssDNA part "http://identifiers.org/kegg.compound/C00271",
                "http://identifiers.org/pirsf/PIRSF002091",
                "http://identifiers.org/chebi/CHEBI:9160"
  RPAssDNA1 part "http://identifiers.org/kegg.compound/C00271",
                 "http://identifiers.org/pirsf/PIRSF002091",
                 "http://identifiers.org/chebi/CHEBI:9160"
  RPAssDNA2 part "http://identifiers.org/kegg.compound/C00271",
                 "http://identifiers.org/pirsf/PIRSF002091",
                 "http://identifiers.org/chebi/CHEBI:9160"
  Mec1RPAssDNA part "http://identifiers.org/uniprot/P38111",
                    "http://identifiers.org/kegg.compound/C00271",
                    "http://identifiers.org/pirsf/PIRSF002091",
                    "http://identifiers.org/chebi/CHEBI:9160"
  ExoXI homolog "http://identifiers.org/uniprot/P0AEK1"
  ExoXA homolog "http://identifiers.org/uniprot/P0AEK1"
  Exo1I identity "http://identifiers.org/uniprot/P39875"
  Exo1A hypernym "http://identifiers.org/uniprot/P39875"
  Rad9I hypernym "http://identifiers.org/uniprot/P14737"
  Rad9A identity "http://identifiers.org/uniprot/P14737"
  Rad53I identity "http://identifiers.org/uniprot/P22216"
  Rad53A hypernym "http://identifiers.org/uniprot/P22216"
  Chk1I identity "http://identifiers.org/uniprot/P38147"
  Chk1A identity "http://identifiers.org/uniprot/P38147"
  Dun1I identity "http://identifiers.org/uniprot/P39009"
  Dun1A identity "http://identifiers.org/uniprot/P39009"
  ATP identity "http://identifiers.org/obo.chebi/CHEBI:15422"
  ADP identity "http://identifiers.org/obo.chebi/CHEBI:16761"
  G1 hypernym "http://identifiers.org/obo.go/GO:0051318"
  S hypernym "http://identifiers.org/obo.go/GO:0000084"
  G2 hypernym "http://identifiers.org/obo.go/GO:0051319"
  M hypernym "http://identifiers.org/obo.go/GO:0000279"
  G1cyclin version "http://identifiers.org/uniprot/P20437"
  Scyclin version "http://identifiers.org/uniprot/P30283"
  G2cyclin version "http://identifiers.org/uniprot/P24868"
  Mcyclin homolog "http://identifiers.org/uniprot/O14332"
  G1CdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
  G1CdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
  SCdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
  SCdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
  G2CdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
  G2CdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
  MCdkI hypernym "http://identifiers.org/obo.go/GO:0019908"
  MCdkA hypernym "http://identifiers.org/obo.go/GO:0019908"
  G1Soff hypernym "http://identifiers.org/obo.go/GO:0031575"
  G1Son hypernym "http://identifiers.org/obo.go/GO:0000082"
  SG2off hypernym "http://identifiers.org/obo.go/GO:0000115"
  SG2on hypernym "http://identifiers.org/obo.go/GO:0000115"
  G2Moff hypernym "http://identifiers.org/obo.go/GO:0031572"
  G2Mon hypernym "http://identifiers.org/obo.go/GO:0000086"
  MG1on hypernym "http://identifiers.org/obo.go/GO:0000087"
  budscar hypernym "http://identifiers.org/obo.go/GO:0005621"
  Capping hypernym "http://identifiers.org/obo.go/GO:0016233"
  Uncapping hypernym "http://identifiers.org/obo.go/GO:0043241"
  Rad17binding hypernym "http://identifiers.org/obo.go/GO:0005515",
                        "http://identifiers.org/obo.go/GO:0016887"
  ExoXactivation hypernym "http://identifiers.org/obo.go/GO:0032075"
  ExoXactivity hypernym "http://identifiers.org/obo.go/GO:0008856"
  ExoXactivity hypernym "http://identifiers.org/ec-code/3.1.11.1"
  Exo1activation hypernym "http://identifiers.org/obo.go/GO:0032075"
  Exo1Rad24dependentActivation hypernym "http://identifiers.org/obo.go/GO:0032075"
  Exo1Rad17independentActivity hypernym "http://identifiers.org/obo.go/GO:0008856"
  Exo1Rad17dependentActivity hypernym "http://identifiers.org/obo.go/GO:0008856"
  RPAbinding1 hypernym "http://identifiers.org/obo.go/GO:0003676",
                       "http://identifiers.org/obo.go/GO:0005515"
  RPAbinding2 hypernym "http://identifiers.org/obo.go/GO:0003676",
                       "http://identifiers.org/obo.go/GO:0032403"
  RPAbinding hypernym "http://identifiers.org/obo.go/GO:0003676",
                      "http://identifiers.org/obo.go/GO:0032403"
  Mec1binding hypernym "http://identifiers.org/obo.go/GO:0005515"
  Mec1binding hypernym "http://identifiers.org/obo.go/GO:0006461"
  Rad9activation hypernym "http://identifiers.org/obo.go/GO:0030295"
  ExoXinhibition hypernym "http://identifiers.org/obo.go/GO:0004860"
  ExoXinhibition2 hypernym "http://identifiers.org/obo.go/GO:0004860"
  Rad53activation hypernym "http://identifiers.org/obo.go/GO:0030295"
  Chk1Activation hypernym "http://identifiers.org/obo.go/GO:0030295"
  Exo1inhibition hypernym "http://identifiers.org/obo.go/GO:0004860"
  Dun1activation hypernym "http://identifiers.org/obo.go/GO:0030295"
  Chk1cellArrest hypernym "http://identifiers.org/obo.go/GO:0007050"
  Dun1cellArrest hypernym "http://identifiers.org/obo.go/GO:0007050"
  SDNArepair1 hypernym "http://identifiers.org/obo.go/GO:0043241"
  SDNArepair1 hypernym "http://identifiers.org/obo.go/GO:0006281"
  G2DNArepair1 hypernym "http://identifiers.org/obo.go/GO:0043241"
  G2DNArepair1 hypernym "http://identifiers.org/obo.go/GO:0006281"
  SDNArepair2 hypernym "http://identifiers.org/obo.go/GO:0006308"
  G2DNArepair2 hypernym "http://identifiers.org/obo.go/GO:0006308"
  Recovery hypernym "http://identifiers.org/obo.go/GO:0005515",
                    "http://identifiers.org/obo.go/GO:0016233"
  G1cyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  ScyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  G2cyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  McyclinSynthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  G1toSGenesOn hypernym "http://identifiers.org/obo.go/GO:0007089"
  G2toMGenesOn hypernym "http://identifiers.org/obo.go/GO:0031572"
  G1cyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
  ScyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
  G2cyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
  McyclinDegradation hypernym "http://identifiers.org/obo.go/GO:0008054"
  G1toSProgession hypernym "http://identifiers.org/obo.go/GO:0000082"
  G2toMProgession hypernym "http://identifiers.org/obo.go/GO:0000086"
  MtoG1Progession hypernym "http://identifiers.org/obo.go/GO:0000216"
end

YeastWTmodel2 is "Proctor2006_telomere"

YeastWTmodel2 model_entity_is "http://identifiers.org/biomodels.db/MODEL8679489165"
YeastWTmodel2 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000087"
YeastWTmodel2 description "http://identifiers.org/pubmed/17015293"
YeastWTmodel2 taxon "http://identifiers.org/taxonomy/4932"
YeastWTmodel2 parthood "http://identifiers.org/kegg.pathway/sce04111"
YeastWTmodel2 hypernym "http://identifiers.org/obo.go/GO:0000075"
