
-------------------------------------------------- Run --------------------------------------------------
MaBoSS version: 2.4.1 [networks up to 64 nodes]

Run start time: Wed Oct 19 16:10:24 2022
Run end time: Wed Oct 19 16:10:24 2022

Core user runtime: 0.02 secs using 6 threads
Core elapsed runtime: 0.011 secs using 6 threads

Epilogue user runtime: 0 secs using 1 thread
Epilogue elapsed runtime: 0 secs using 1 thread

StatDist user runtime: 0 secs using 1 thread
StatDist elapsed runtime: 0 secs using 1 thread

Time Tick: 0.05
Max Time: 5
Sample Count: 100
StatDist Trajectory Count: 0
StatDist Similarity Cache Maximum Size: 20000
Discrete Time: FALSE
Random Generator: physical
Generated Number Count: 8006

---------------------------------------------------------------------------------------------------------

------------------------------------------------ Network ------------------------------------------------
node HTRA2 {
  rate_up = 0;
  rate_down = $u_HTRA2;
}

node AKT1_phosphorylated {
  rate_up = 0;
  rate_down = $u_AKT1_phosphorylated;
}

node PINK1 {
  rate_up = 0;
  rate_down = $u_PINK1;
}

node SNCA {
  rate_up = 0;
  rate_down = $u_SNCA;
}

node AMPK_complex_neuron {
  rate_up = 0;
  rate_down = $u_AMPK_complex_neuron;
}

node CLPP {
  rate_up = 0;
  rate_down = $u_CLPP;
}

node mt_UPR_phenotype {
  logic = (((NOT CLPP AND generic_protein_mitochondrial_matrix)) OR (CLPP));
  rate_up = (@logic ? $u_mt_UPR_phenotype : 0);
  rate_down = (@logic ? 0 : $d_mt_UPR_phenotype);
}

node MAPK9_mitochondrial_matrix {
  logic = (mt_UPR_phenotype);
  rate_up = (@logic ? $u_MAPK9_mitochondrial_matrix : 0);
  rate_down = (@logic ? 0 : $d_MAPK9_mitochondrial_matrix);
}

node HSPD1 {
  rate_up = 0;
  rate_down = $u_HSPD1;
}

node HSPE1 {
  rate_up = 0;
  rate_down = $u_HSPE1;
}

node ROS_simple_molecule_mitochondrial_matrix {
  rate_up = 0;
  rate_down = $u_ROS_simple_molecule_mitochondrial_matrix;
}

node generic_protein_mitochondrial_matrix {
  logic = ((((NOT HTRA2) OR ((((HTRA2 AND NOT HSPD1) AND NOT HSPE1) AND generic_protein_mitochondrial_matrix))) OR (((HTRA2 AND NOT HSPD1) AND HSPE1))) OR ((HTRA2 AND HSPD1)));
  rate_up = (@logic ? $u_generic_protein_mitochondrial_matrix : 0);
  rate_down = (@logic ? 0 : $d_generic_protein_mitochondrial_matrix);
}

node MAPK8 {
  rate_up = 0;
  rate_down = $u_MAPK8;
}

node neuron {
  logic = (((NOT MAPK8 AND neuron)) OR (MAPK8));
  rate_up = (@logic ? $u_neuron : 0);
  rate_down = (@logic ? 0 : $d_neuron);
}

node ROS_simple_molecule_neuron {
  rate_up = 0;
  rate_down = $u_ROS_simple_molecule_neuron;
}

node MAP3K5 {
  logic = (ROS_simple_molecule_neuron);
  rate_up = (@logic ? $u_MAP3K5 : 0);
  rate_down = (@logic ? 0 : $d_MAP3K5);
}

node SIRT3 {
  logic = (((((NOT ROS_simple_molecule_mitochondrial_matrix AND NOT generic_protein_mitochondrial_matrix) AND SIRT3)) OR ((NOT ROS_simple_molecule_mitochondrial_matrix AND generic_protein_mitochondrial_matrix))) OR (ROS_simple_molecule_mitochondrial_matrix));
  rate_up = (@logic ? $u_SIRT3 : 0);
  rate_down = (@logic ? 0 : $d_SIRT3);
}

node FOXO3_mitochondrial_matrix {
  logic = (SIRT3);
  rate_up = (@logic ? $u_FOXO3_mitochondrial_matrix : 0);
  rate_down = (@logic ? 0 : $d_FOXO3_mitochondrial_matrix);
}

node DDIT3 {
  rate_up = 0;
  rate_down = $u_DDIT3;
}

node FOXO3_nucleus {
  logic = (((NOT SIRT3 AND FOXO3_mitochondrial_matrix)) OR (SIRT3));
  rate_up = (@logic ? $u_FOXO3_nucleus : 0);
  rate_down = (@logic ? 0 : $d_FOXO3_nucleus);
}

node TF_CHOP_FOXO_complex {
  logic = (((NOT DDIT3 AND FOXO3_nucleus)) OR (DDIT3));
  rate_up = (@logic ? $u_TF_CHOP_FOXO_complex : 0);
  rate_down = (@logic ? 0 : $d_TF_CHOP_FOXO_complex);
}

node PPARGC1A_phosphorylated {
  rate_up = 0;
  rate_down = $u_PPARGC1A_phosphorylated;
}

node TF_FOXO3_complex_nucleus {
  logic = (((((((((((((((NOT PPARGC1A_phosphorylated AND NOT FOXO3_neuron) AND NOT SIRT1) AND NOT SIRT2) AND NOT MAPK9_phosphorylated) AND NOT AMPK_complex_nucleus) AND NOT FOXO3_acetylated_phosphorylated) AND TF_FOXO3_complex_nucleus)) OR (((((((NOT PPARGC1A_phosphorylated AND NOT FOXO3_neuron) AND NOT SIRT1) AND NOT SIRT2) AND NOT MAPK9_phosphorylated) AND NOT AMPK_complex_nucleus) AND FOXO3_acetylated_phosphorylated))) OR ((((((NOT PPARGC1A_phosphorylated AND NOT FOXO3_neuron) AND NOT SIRT1) AND NOT SIRT2) AND NOT MAPK9_phosphorylated) AND AMPK_complex_nucleus))) OR (((((NOT PPARGC1A_phosphorylated AND NOT FOXO3_neuron) AND NOT SIRT1) AND NOT SIRT2) AND MAPK9_phosphorylated))) OR ((((NOT PPARGC1A_phosphorylated AND NOT FOXO3_neuron) AND NOT SIRT1) AND SIRT2))) OR (((NOT PPARGC1A_phosphorylated AND NOT FOXO3_neuron) AND SIRT1))) OR ((NOT PPARGC1A_phosphorylated AND FOXO3_neuron))) OR (PPARGC1A_phosphorylated));
  rate_up = (@logic ? $u_TF_FOXO3_complex_nucleus : 0);
  rate_down = (@logic ? 0 : $d_TF_FOXO3_complex_nucleus);
}

node CAT_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_CAT_rna : 0);
  rate_down = (@logic ? 0 : $d_CAT_rna);
}

node EIF4EBP1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_EIF4EBP1_rna : 0);
  rate_down = (@logic ? 0 : $d_EIF4EBP1_rna);
}

node DNM1L_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_DNM1L_rna : 0);
  rate_down = (@logic ? 0 : $d_DNM1L_rna);
}

node BECN1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_BECN1_rna : 0);
  rate_down = (@logic ? 0 : $d_BECN1_rna);
}

node FIS1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_FIS1_rna : 0);
  rate_down = (@logic ? 0 : $d_FIS1_rna);
}

node TFAM_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_TFAM_rna : 0);
  rate_down = (@logic ? 0 : $d_TFAM_rna);
}

node MAP1LC3A_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_MAP1LC3A_rna : 0);
  rate_down = (@logic ? 0 : $d_MAP1LC3A_rna);
}

node MUL1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_MUL1_rna : 0);
  rate_down = (@logic ? 0 : $d_MUL1_rna);
}

node GABARAPL1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_GABARAPL1_rna : 0);
  rate_down = (@logic ? 0 : $d_GABARAPL1_rna);
}

node ATG12_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_ATG12_rna : 0);
  rate_down = (@logic ? 0 : $d_ATG12_rna);
}

node MFN2_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_MFN2_rna : 0);
  rate_down = (@logic ? 0 : $d_MFN2_rna);
}

node SOD2_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_SOD2_rna : 0);
  rate_down = (@logic ? 0 : $d_SOD2_rna);
}

node BNIP3_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_BNIP3_rna : 0);
  rate_down = (@logic ? 0 : $d_BNIP3_rna);
}

node GPX1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_GPX1_rna : 0);
  rate_down = (@logic ? 0 : $d_GPX1_rna);
}

node BNIP3L_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_BNIP3L_rna : 0);
  rate_down = (@logic ? 0 : $d_BNIP3L_rna);
}

node MAPK9_nucleus {
  logic = (MAPK9_mitochondrial_matrix);
  rate_up = (@logic ? $u_MAPK9_nucleus : 0);
  rate_down = (@logic ? 0 : $d_MAPK9_nucleus);
}

node JUN {
  rate_up = 0;
  rate_down = $u_JUN;
}

node TF_AP_1_complex {
  logic = (((NOT MAPK9_nucleus AND JUN)) OR (MAPK9_nucleus));
  rate_up = (@logic ? $u_TF_AP_1_complex : 0);
  rate_down = (@logic ? 0 : $d_TF_AP_1_complex);
}

node FOXO3_neuron {
  logic = (AMPK_complex_neuron);
  rate_up = (@logic ? $u_FOXO3_neuron : 0);
  rate_down = (@logic ? 0 : $d_FOXO3_neuron);
}

node SIRT1 {
  logic = (PINK1);
  rate_up = (@logic ? $u_SIRT1 : 0);
  rate_down = (@logic ? 0 : $d_SIRT1);
}

node SIRT2 {
  rate_up = 0;
  rate_down = $u_SIRT2;
}

node MAPK9_phosphorylated {
  logic = (MAP3K5);
  rate_up = (@logic ? $u_MAPK9_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_MAPK9_phosphorylated);
}

node AMPK_complex_nucleus {
  rate_up = 0;
  rate_down = $u_AMPK_complex_nucleus;
}

node FOXO3_acetylated_phosphorylated {
  logic = (((((((NOT AKT1_phosphorylated AND NOT neuron) AND NOT FOXO3_acetylated_phosphorylated) AND TF_FOXO3_complex_nucleus)) OR (((NOT AKT1_phosphorylated AND NOT neuron) AND FOXO3_acetylated_phosphorylated))) OR ((NOT AKT1_phosphorylated AND neuron))) OR (AKT1_phosphorylated));
  rate_up = (@logic ? $u_FOXO3_acetylated_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_FOXO3_acetylated_phosphorylated);
}

node PPARGC1A_rna {
  logic = ((NOT SNCA) OR ((SNCA AND TF_FOXO3_complex_nucleus)));
  rate_up = (@logic ? $u_PPARGC1A_rna : 0);
  rate_down = (@logic ? 0 : $d_PPARGC1A_rna);
}

node TXNIP_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_TXNIP_rna : 0);
  rate_down = (@logic ? 0 : $d_TXNIP_rna);
}

node FASLG_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_FASLG_rna : 0);
  rate_down = (@logic ? 0 : $d_FASLG_rna);
}

node BCL2L11_rna {
  logic = (((NOT TF_CHOP_FOXO_complex AND TF_FOXO3_complex_nucleus)) OR (TF_CHOP_FOXO_complex));
  rate_up = (@logic ? $u_BCL2L11_rna : 0);
  rate_down = (@logic ? 0 : $d_BCL2L11_rna);
}

node BBC3_rna {
  logic = (((NOT TF_CHOP_FOXO_complex AND TF_FOXO3_complex_nucleus)) OR (TF_CHOP_FOXO_complex));
  rate_up = (@logic ? $u_BBC3_rna : 0);
  rate_down = (@logic ? 0 : $d_BBC3_rna);
}

node MAPK14_phosphorylated {
  logic = (MAP3K5);
  rate_up = (@logic ? $u_MAPK14_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_MAPK14_phosphorylated);
}

node response_to_oxidative_stress_phenotype {
  logic = (((((NOT CAT_rna AND NOT SOD2_rna) AND GPX1_rna)) OR ((NOT CAT_rna AND SOD2_rna))) OR (CAT_rna));
  rate_up = (@logic ? $u_response_to_oxidative_stress_phenotype : 0);
  rate_down = (@logic ? 0 : $d_response_to_oxidative_stress_phenotype);
}

node translation_phenotype {
  logic = (NOT EIF4EBP1_rna);
  rate_up = (@logic ? $u_translation_phenotype : 0);
  rate_down = (@logic ? 0 : $d_translation_phenotype);
}

node Fission_Fusion_phenotype {
  logic = (((((NOT DNM1L_rna AND NOT FIS1_rna) AND MFN2_rna)) OR ((NOT DNM1L_rna AND FIS1_rna))) OR (DNM1L_rna));
  rate_up = (@logic ? $u_Fission_Fusion_phenotype : 0);
  rate_down = (@logic ? 0 : $d_Fission_Fusion_phenotype);
}

node autophagy_phenotype {
  logic = (((((((((((((NOT BECN1_rna AND NOT MAP1LC3A_rna) AND NOT MUL1_rna) AND NOT GABARAPL1_rna) AND NOT ATG12_rna) AND NOT BNIP3_rna) AND BNIP3L_rna)) OR ((((((NOT BECN1_rna AND NOT MAP1LC3A_rna) AND NOT MUL1_rna) AND NOT GABARAPL1_rna) AND NOT ATG12_rna) AND BNIP3_rna))) OR (((((NOT BECN1_rna AND NOT MAP1LC3A_rna) AND NOT MUL1_rna) AND NOT GABARAPL1_rna) AND ATG12_rna))) OR ((((NOT BECN1_rna AND NOT MAP1LC3A_rna) AND NOT MUL1_rna) AND GABARAPL1_rna))) OR (((NOT BECN1_rna AND NOT MAP1LC3A_rna) AND MUL1_rna))) OR ((NOT BECN1_rna AND MAP1LC3A_rna))) OR (BECN1_rna));
  rate_up = (@logic ? $u_autophagy_phenotype : 0);
  rate_down = (@logic ? 0 : $d_autophagy_phenotype);
}

node mitochondrial_biogenesis_phenotype {
  logic = (((NOT TFAM_rna AND PPARGC1A_rna)) OR (TFAM_rna));
  rate_up = (@logic ? $u_mitochondrial_biogenesis_phenotype : 0);
  rate_down = (@logic ? 0 : $d_mitochondrial_biogenesis_phenotype);
}

node DDIT3_rna {
  logic = (TF_AP_1_complex);
  rate_up = (@logic ? $u_DDIT3_rna : 0);
  rate_down = (@logic ? 0 : $d_DDIT3_rna);
}

node CEBPB_rna {
  logic = (TF_AP_1_complex);
  rate_up = (@logic ? $u_CEBPB_rna : 0);
  rate_down = (@logic ? 0 : $d_CEBPB_rna);
}

node apoptosis_phenotype {
  logic = (((((((NOT TXNIP_rna AND NOT FASLG_rna) AND NOT BCL2L11_rna) AND BBC3_rna)) OR (((NOT TXNIP_rna AND NOT FASLG_rna) AND BCL2L11_rna))) OR ((NOT TXNIP_rna AND FASLG_rna))) OR (TXNIP_rna));
  rate_up = (@logic ? $u_apoptosis_phenotype : 0);
  rate_down = (@logic ? 0 : $d_apoptosis_phenotype);
}

node PINK1_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_PINK1_rna : 0);
  rate_down = (@logic ? 0 : $d_PINK1_rna);
}

node SESN3_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_SESN3_rna : 0);
  rate_down = (@logic ? 0 : $d_SESN3_rna);
}

node RICTOR_rna {
  logic = (TF_FOXO3_complex_nucleus);
  rate_up = (@logic ? $u_RICTOR_rna : 0);
  rate_down = (@logic ? 0 : $d_RICTOR_rna);
}
---------------------------------------------------------------------------------------------------------

----------------------------------------------- Variables -----------------------------------------------
$High_BNIP3_rna = 0;
$High_DNM1L_rna = 1;
$High_GABARAPL1_rna = 1;
$High_PINK1 = 0;
$High_PINK1_rna = 0;
$High_SIRT1 = 1;
$High_SNCA = 0;
$High_TXNIP_rna = 0;
$Low_BNIP3_rna = 1;
$Low_DNM1L_rna = 0;
$Low_GABARAPL1_rna = 0;
$Low_PINK1 = 1;
$Low_PINK1_rna = 1;
$Low_SIRT1 = 0;
$Low_SNCA = 1;
$Low_TXNIP_rna = 1;
$d_AKT1_phosphorylated = 1;
$d_AMPK_complex_neuron = 1;
$d_AMPK_complex_nucleus = 1;
$d_ATG12_rna = 1;
$d_BBC3_rna = 1;
$d_BCL2L11_rna = 1;
$d_BECN1_rna = 1;
$d_BNIP3L_rna = 1;
$d_BNIP3_rna = 1;
$d_CAT_rna = 1;
$d_CEBPB_rna = 1;
$d_CLPP = 1;
$d_DDIT3 = 1;
$d_DDIT3_rna = 1;
$d_DNM1L_rna = 1;
$d_EIF4EBP1_rna = 1;
$d_FASLG_rna = 1;
$d_FIS1_rna = 1;
$d_FOXO3_acetylated_phosphorylated = 1;
$d_FOXO3_mitochondrial_matrix = 1;
$d_FOXO3_neuron = 1;
$d_FOXO3_nucleus = 1;
$d_Fission_Fusion_phenotype = 1;
$d_GABARAPL1_rna = 1;
$d_GPX1_rna = 1;
$d_HSPD1 = 1;
$d_HSPE1 = 1;
$d_HTRA2 = 1;
$d_JUN = 1;
$d_MAP1LC3A_rna = 1;
$d_MAP3K5 = 1;
$d_MAPK14_phosphorylated = 1;
$d_MAPK8 = 1;
$d_MAPK9_mitochondrial_matrix = 1;
$d_MAPK9_nucleus = 1;
$d_MAPK9_phosphorylated = 1;
$d_MFN2_rna = 1;
$d_MUL1_rna = 1;
$d_PINK1 = 1;
$d_PINK1_rna = 1;
$d_PPARGC1A_phosphorylated = 1;
$d_PPARGC1A_rna = 1;
$d_RICTOR_rna = 1;
$d_ROS_simple_molecule_mitochondrial_matrix = 1;
$d_ROS_simple_molecule_neuron = 1;
$d_SESN3_rna = 1;
$d_SIRT1 = 1;
$d_SIRT2 = 1;
$d_SIRT3 = 1;
$d_SNCA = 1;
$d_SOD2_rna = 1;
$d_TFAM_rna = 1;
$d_TF_AP_1_complex = 1;
$d_TF_CHOP_FOXO_complex = 1;
$d_TF_FOXO3_complex_nucleus = 1;
$d_TXNIP_rna = 1;
$d_apoptosis_phenotype = 1;
$d_autophagy_phenotype = 1;
$d_generic_protein_mitochondrial_matrix = 1;
$d_mitochondrial_biogenesis_phenotype = 1;
$d_mt_UPR_phenotype = 1;
$d_neuron = 1;
$d_response_to_oxidative_stress_phenotype = 1;
$d_translation_phenotype = 1;
$nb_mutable = 0;
$u_AKT1_phosphorylated = 1;
$u_AMPK_complex_neuron = 1;
$u_AMPK_complex_nucleus = 1;
$u_ATG12_rna = 1;
$u_BBC3_rna = 1;
$u_BCL2L11_rna = 1;
$u_BECN1_rna = 1;
$u_BNIP3L_rna = 1;
$u_BNIP3_rna = 1;
$u_CAT_rna = 1;
$u_CEBPB_rna = 1;
$u_CLPP = 1;
$u_DDIT3 = 1;
$u_DDIT3_rna = 1;
$u_DNM1L_rna = 1;
$u_EIF4EBP1_rna = 1;
$u_FASLG_rna = 1;
$u_FIS1_rna = 1;
$u_FOXO3_acetylated_phosphorylated = 1;
$u_FOXO3_mitochondrial_matrix = 1;
$u_FOXO3_neuron = 1;
$u_FOXO3_nucleus = 1;
$u_Fission_Fusion_phenotype = 1;
$u_GABARAPL1_rna = 1;
$u_GPX1_rna = 1;
$u_HSPD1 = 1;
$u_HSPE1 = 1;
$u_HTRA2 = 1;
$u_JUN = 1;
$u_MAP1LC3A_rna = 1;
$u_MAP3K5 = 1;
$u_MAPK14_phosphorylated = 1;
$u_MAPK8 = 1;
$u_MAPK9_mitochondrial_matrix = 1;
$u_MAPK9_nucleus = 1;
$u_MAPK9_phosphorylated = 1;
$u_MFN2_rna = 1;
$u_MUL1_rna = 1;
$u_PINK1 = 1;
$u_PINK1_rna = 1;
$u_PPARGC1A_phosphorylated = 1;
$u_PPARGC1A_rna = 1;
$u_RICTOR_rna = 1;
$u_ROS_simple_molecule_mitochondrial_matrix = 1;
$u_ROS_simple_molecule_neuron = 1;
$u_SESN3_rna = 1;
$u_SIRT1 = 1;
$u_SIRT2 = 1;
$u_SIRT3 = 1;
$u_SNCA = 1;
$u_SOD2_rna = 1;
$u_TFAM_rna = 1;
$u_TF_AP_1_complex = 1;
$u_TF_CHOP_FOXO_complex = 1;
$u_TF_FOXO3_complex_nucleus = 1;
$u_TXNIP_rna = 1;
$u_apoptosis_phenotype = 1;
$u_autophagy_phenotype = 1;
$u_generic_protein_mitochondrial_matrix = 1;
$u_mitochondrial_biogenesis_phenotype = 1;
$u_mt_UPR_phenotype = 1;
$u_neuron = 1;
$u_response_to_oxidative_stress_phenotype = 1;
$u_translation_phenotype = 1;
---------------------------------------------------------------------------------------------------------

