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

Run start time: Wed Oct 19 12:54:32 2022
Run end time: Wed Oct 19 12:54:32 2022

Core user runtime: 0.01 secs using 6 threads
Core elapsed runtime: 0.004 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: 3591

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

------------------------------------------------ Network ------------------------------------------------
node GABARAPL1_neuron {
  rate_up = 0;
  rate_down = $u_GABARAPL1_neuron;
}

node PMPCB {
  rate_up = 0;
  rate_down = $u_PMPCB;
}

node PMPCA {
  rate_up = 0;
  rate_down = $u_PMPCA;
}

node SNCA_neuron {
  rate_up = 0;
  rate_down = $u_SNCA_neuron;
}

node BAG2 {
  rate_up = 0;
  rate_down = $u_BAG2;
}

node BAG5 {
  rate_up = 0;
  rate_down = $u_BAG5;
}

node NEDD8 {
  rate_up = 0;
  rate_down = $u_NEDD8;
}

node PARL {
  rate_up = 0;
  rate_down = $u_PARL;
}

node OPTN {
  rate_up = 0;
  rate_down = $u_OPTN;
}

node GABARAP {
  rate_up = 0;
  rate_down = $u_GABARAP;
}

node ATG13_phosphorylated {
  rate_up = 0;
  rate_down = $u_ATG13_phosphorylated;
}

node BNIP3L {
  rate_up = 0;
  rate_down = $u_BNIP3L;
}

node GABARAPL1_mitochondrion {
  logic = (((NOT GABARAPL1_neuron AND BNIP3L)) OR (GABARAPL1_neuron));
  rate_up = (@logic ? $u_GABARAPL1_mitochondrion : 0);
  rate_down = (@logic ? 0 : $d_GABARAPL1_mitochondrion);
}

node MAP1LC3A_neuron {
  rate_up = 0;
  rate_down = $u_MAP1LC3A_neuron;
}

node MAP1LC3A_mitochondrion {
  logic = (((NOT BNIP3L AND MAP1LC3A_neuron)) OR (BNIP3L));
  rate_up = (@logic ? $u_MAP1LC3A_mitochondrion : 0);
  rate_down = (@logic ? 0 : $d_MAP1LC3A_mitochondrion);
}

node HSP90 {
  rate_up = 0;
  rate_down = $u_HSP90;
}

node MARK2 {
  rate_up = 0;
  rate_down = $u_MARK2;
}

node PGAM5 {
  rate_up = 0;
  rate_down = $u_PGAM5;
}

node mitochondrial_depolarization_phenotype {
  rate_up = 0;
  rate_down = $u_mitochondrial_depolarization_phenotype;
}

node TIM_Complex_complex {
  rate_up = 0;
  rate_down = $u_TIM_Complex_complex;
}

node TOM_complex_complex {
  rate_up = 0;
  rate_down = $u_TOM_complex_complex;
}

node ATXN3 {
  rate_up = 0;
  rate_down = $u_ATXN3;
}

node PINK1_neuron {
  logic = ((((NOT BAG2) OR ((BAG2 AND NOT BAG5))) OR ((((BAG2 AND BAG5) AND NOT NEDD8) AND PINK1_neuron))) OR (((BAG2 AND BAG5) AND NEDD8)));
  rate_up = (@logic ? $u_PINK1_neuron : 0);
  rate_down = (@logic ? 0 : $d_PINK1_neuron);
}

node ubiquitin_phosphorylated {
  logic = (PINK1_neuron);
  rate_up = (@logic ? $u_ubiquitin_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_ubiquitin_phosphorylated);
}

node PRKN {
  rate_up = 0;
  rate_down = $u_PRKN;
}

node HSPA9 {
  rate_up = 0;
  rate_down = $u_HSPA9;
}

node PARK7_neuron {
  rate_up = 0;
  rate_down = $u_PARK7_neuron;
}

node VPS13C {
  rate_up = 0;
  rate_down = $u_VPS13C;
}

node ROS {
  rate_up = 0;
  rate_down = $u_ROS;
}

node CCCP {
  rate_up = 0;
  rate_down = $u_CCCP;
}

node FBXO7 {
  rate_up = 0;
  rate_down = $u_FBXO7;
}

node SIAH3 {
  rate_up = 0;
  rate_down = $u_SIAH3;
}

node BAG4 {
  rate_up = 0;
  rate_down = $u_BAG4;
}

node HSPA1L {
  rate_up = 0;
  rate_down = $u_HSPA1L;
}

node fatty_acid {
  rate_up = 0;
  rate_down = $u_fatty_acid;
}

node cholesterol {
  rate_up = 0;
  rate_down = $u_cholesterol;
}

node FBXW7 {
  rate_up = 0;
  rate_down = $u_FBXW7;
}

node SREBF1 {
  logic = (FBXW7);
  rate_up = (@logic ? $u_SREBF1 : 0);
  rate_down = (@logic ? 0 : $d_SREBF1);
}

node PINK1_mitochondrion {
  logic = ((((((((((((NOT HSP90 AND NOT MARK2) AND NOT PGAM5) AND NOT mitochondrial_depolarization_phenotype)) OR (((((((((NOT HSP90 AND NOT MARK2) AND NOT PGAM5) AND mitochondrial_depolarization_phenotype) AND NOT TIM_Complex_complex) AND NOT TOM_complex_complex) AND NOT PINK1_neuron) AND NOT SREBF1) AND PINK1_mitochondrion))) OR ((((((((NOT HSP90 AND NOT MARK2) AND NOT PGAM5) AND mitochondrial_depolarization_phenotype) AND NOT TIM_Complex_complex) AND NOT TOM_complex_complex) AND NOT PINK1_neuron) AND SREBF1))) OR (((((((NOT HSP90 AND NOT MARK2) AND NOT PGAM5) AND mitochondrial_depolarization_phenotype) AND NOT TIM_Complex_complex) AND NOT TOM_complex_complex) AND PINK1_neuron))) OR ((((((NOT HSP90 AND NOT MARK2) AND NOT PGAM5) AND mitochondrial_depolarization_phenotype) AND NOT TIM_Complex_complex) AND TOM_complex_complex))) OR (((((NOT HSP90 AND NOT MARK2) AND NOT PGAM5) AND mitochondrial_depolarization_phenotype) AND TIM_Complex_complex))) OR (((NOT HSP90 AND NOT MARK2) AND PGAM5))) OR ((NOT HSP90 AND MARK2))) OR (HSP90));
  rate_up = (@logic ? $u_PINK1_mitochondrion : 0);
  rate_down = (@logic ? 0 : $d_PINK1_mitochondrion);
}

node PINK1 {
  logic = (((((((((NOT PMPCB AND NOT PMPCA) AND NOT PARL) AND NOT HSP90) AND PINK1_mitochondrion)) OR ((((NOT PMPCB AND NOT PMPCA) AND NOT PARL) AND HSP90))) OR (((NOT PMPCB AND NOT PMPCA) AND PARL))) OR ((NOT PMPCB AND PMPCA))) OR (PMPCB));
  rate_up = (@logic ? $u_PINK1 : 0);
  rate_down = (@logic ? 0 : $d_PINK1);
}

node PRKN_ubiquitinated {
  logic = (((((((NOT ATXN3 AND NOT ubiquitin_phosphorylated) AND NOT PINK1_neuron) AND PRKN)) OR (((NOT ATXN3 AND NOT ubiquitin_phosphorylated) AND PINK1_neuron))) OR ((NOT ATXN3 AND ubiquitin_phosphorylated))) OR (ATXN3));
  rate_up = (@logic ? $u_PRKN_ubiquitinated : 0);
  rate_down = (@logic ? 0 : $d_PRKN_ubiquitinated);
}

node PINK1_PRKN_complex_mitochondrion {
  logic = ((((((((((((((NOT VPS13C) OR (((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND NOT SIAH3))) OR ((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND NOT BAG4))) OR ((((((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND NOT fatty_acid) AND NOT cholesterol) AND NOT FBXW7) AND NOT SREBF1) AND NOT PINK1))) OR ((((((((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND NOT fatty_acid) AND NOT cholesterol) AND NOT FBXW7) AND NOT SREBF1) AND PINK1) AND NOT PINK1_mitochondrion) AND PRKN_ubiquitinated))) OR (((((((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND NOT fatty_acid) AND NOT cholesterol) AND NOT FBXW7) AND NOT SREBF1) AND PINK1) AND PINK1_mitochondrion))) OR (((((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND NOT fatty_acid) AND NOT cholesterol) AND NOT FBXW7) AND SREBF1))) OR ((((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND NOT fatty_acid) AND NOT cholesterol) AND FBXW7))) OR (((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND NOT fatty_acid) AND cholesterol))) OR ((((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND NOT HSPA1L) AND fatty_acid))) OR (((((((VPS13C AND NOT ROS) AND NOT CCCP) AND NOT FBXO7) AND SIAH3) AND BAG4) AND HSPA1L))) OR ((((VPS13C AND NOT ROS) AND NOT CCCP) AND FBXO7))) OR (((VPS13C AND NOT ROS) AND CCCP))) OR ((VPS13C AND ROS)));
  rate_up = (@logic ? $u_PINK1_PRKN_complex_mitochondrion : 0);
  rate_down = (@logic ? 0 : $d_PINK1_PRKN_complex_mitochondrion);
}

node BCL2L1_BAX_complex {
  rate_up = 0;
  rate_down = $u_BCL2L1_BAX_complex;
}

node PARK7_mitochondrion {
  logic = (((NOT HSPA9 AND PARK7_neuron)) OR (HSPA9));
  rate_up = (@logic ? $u_PARK7_mitochondrion : 0);
  rate_down = (@logic ? 0 : $d_PARK7_mitochondrion);
}

node DNM1L {
  logic = (oxidized_PARK7_dimer_complex);
  rate_up = (@logic ? $u_DNM1L : 0);
  rate_down = (@logic ? 0 : $d_DNM1L);
}

node oxidized_PARK7_dimer_complex {
  logic = (PARK7_mitochondrion);
  rate_up = (@logic ? $u_oxidized_PARK7_dimer_complex : 0);
  rate_down = (@logic ? 0 : $d_oxidized_PARK7_dimer_complex);
}

node mitophagy_phenotype {
  logic = (((((((((((((((((NOT OPTN AND NOT GABARAP) AND NOT ATG13_phosphorylated) AND NOT GABARAPL1_mitochondrion) AND NOT MAP1LC3A_mitochondrion) AND NOT PRKN_ubiquitinated) AND NOT PINK1_PRKN_complex_mitochondrion) AND NOT DNM1L) AND oxidized_PARK7_dimer_complex)) OR ((((((((NOT OPTN AND NOT GABARAP) AND NOT ATG13_phosphorylated) AND NOT GABARAPL1_mitochondrion) AND NOT MAP1LC3A_mitochondrion) AND NOT PRKN_ubiquitinated) AND NOT PINK1_PRKN_complex_mitochondrion) AND DNM1L))) OR (((((((NOT OPTN AND NOT GABARAP) AND NOT ATG13_phosphorylated) AND NOT GABARAPL1_mitochondrion) AND NOT MAP1LC3A_mitochondrion) AND NOT PRKN_ubiquitinated) AND PINK1_PRKN_complex_mitochondrion))) OR ((((((NOT OPTN AND NOT GABARAP) AND NOT ATG13_phosphorylated) AND NOT GABARAPL1_mitochondrion) AND NOT MAP1LC3A_mitochondrion) AND PRKN_ubiquitinated))) OR (((((NOT OPTN AND NOT GABARAP) AND NOT ATG13_phosphorylated) AND NOT GABARAPL1_mitochondrion) AND MAP1LC3A_mitochondrion))) OR ((((NOT OPTN AND NOT GABARAP) AND NOT ATG13_phosphorylated) AND GABARAPL1_mitochondrion))) OR (((NOT OPTN AND NOT GABARAP) AND ATG13_phosphorylated))) OR ((NOT OPTN AND GABARAP))) OR (OPTN));
  rate_up = (@logic ? $u_mitophagy_phenotype : 0);
  rate_down = (@logic ? 0 : $d_mitophagy_phenotype);
}

node SNCA_mitochondrion {
  logic = (((NOT SNCA_neuron AND TOM_complex_complex)) OR (SNCA_neuron));
  rate_up = (@logic ? $u_SNCA_mitochondrion : 0);
  rate_down = (@logic ? 0 : $d_SNCA_mitochondrion);
}

node neuron_death_phenotype {
  logic = (((NOT SNCA_neuron AND mitophagy_phenotype)) OR (SNCA_neuron));
  rate_up = (@logic ? $u_neuron_death_phenotype : 0);
  rate_down = (@logic ? 0 : $d_neuron_death_phenotype);
}

node PGAM5_S {
  logic = (((((NOT PARL AND NOT PGAM5) AND mitochondrial_depolarization_phenotype)) OR ((NOT PARL AND PGAM5))) OR (PARL));
  rate_up = (@logic ? $u_PGAM5_S : 0);
  rate_down = (@logic ? 0 : $d_PGAM5_S);
}

node TOMM20_ubiquitinated {
  logic = (((NOT TOM_complex_complex AND PINK1_PRKN_complex_mitochondrion)) OR (TOM_complex_complex));
  rate_up = (@logic ? $u_TOMM20_ubiquitinated : 0);
  rate_down = (@logic ? 0 : $d_TOMM20_ubiquitinated);
}

node TOMM70 {
  logic = (((NOT TOM_complex_complex AND PINK1_PRKN_complex_mitochondrion)) OR (TOM_complex_complex));
  rate_up = (@logic ? $u_TOMM70 : 0);
  rate_down = (@logic ? 0 : $d_TOMM70);
}

node TOMM40_ubiquitinated {
  logic = (((NOT TOM_complex_complex AND PINK1_PRKN_complex_mitochondrion)) OR (TOM_complex_complex));
  rate_up = (@logic ? $u_TOMM40_ubiquitinated : 0);
  rate_down = (@logic ? 0 : $d_TOMM40_ubiquitinated);
}

node BCL2L1_BAX_PARK7_complex {
  logic = (((NOT BCL2L1_BAX_complex AND PARK7_mitochondrion)) OR (BCL2L1_BAX_complex));
  rate_up = (@logic ? $u_BCL2L1_BAX_PARK7_complex : 0);
  rate_down = (@logic ? 0 : $d_BCL2L1_BAX_PARK7_complex);
}
---------------------------------------------------------------------------------------------------------

----------------------------------------------- Variables -----------------------------------------------
$High_HSPA1L = 0;
$High_PINK1 = 0;
$High_PINK1_PRKN_complex_mitochondrion = 0;
$High_SIAH3 = 0;
$High_SNCA_mitochondrion = 0;
$High_SNCA_neuron = 0;
$Low_HSPA1L = 1;
$Low_PINK1 = 1;
$Low_PINK1_PRKN_complex_mitochondrion = 1;
$Low_SIAH3 = 1;
$Low_SNCA_mitochondrion = 1;
$Low_SNCA_neuron = 1;
$d_ATG13_phosphorylated = 1;
$d_ATXN3 = 1;
$d_BAG2 = 1;
$d_BAG4 = 1;
$d_BAG5 = 1;
$d_BCL2L1_BAX_PARK7_complex = 1;
$d_BCL2L1_BAX_complex = 1;
$d_BNIP3L = 1;
$d_CCCP = 1;
$d_DNM1L = 1;
$d_FBXO7 = 1;
$d_FBXW7 = 1;
$d_GABARAP = 1;
$d_GABARAPL1_mitochondrion = 1;
$d_GABARAPL1_neuron = 1;
$d_HSP90 = 1;
$d_HSPA1L = 1;
$d_HSPA9 = 1;
$d_MAP1LC3A_mitochondrion = 1;
$d_MAP1LC3A_neuron = 1;
$d_MARK2 = 1;
$d_NEDD8 = 1;
$d_OPTN = 1;
$d_PARK7_mitochondrion = 1;
$d_PARK7_neuron = 1;
$d_PARL = 1;
$d_PGAM5 = 1;
$d_PGAM5_S = 1;
$d_PINK1 = 1;
$d_PINK1_PRKN_complex_mitochondrion = 1;
$d_PINK1_mitochondrion = 1;
$d_PINK1_neuron = 1;
$d_PMPCA = 1;
$d_PMPCB = 1;
$d_PRKN = 1;
$d_PRKN_ubiquitinated = 1;
$d_ROS = 1;
$d_SIAH3 = 1;
$d_SNCA_mitochondrion = 1;
$d_SNCA_neuron = 1;
$d_SREBF1 = 1;
$d_TIM_Complex_complex = 1;
$d_TOMM20_ubiquitinated = 1;
$d_TOMM40_ubiquitinated = 1;
$d_TOMM70 = 1;
$d_TOM_complex_complex = 1;
$d_VPS13C = 1;
$d_cholesterol = 1;
$d_fatty_acid = 1;
$d_mitochondrial_depolarization_phenotype = 1;
$d_mitophagy_phenotype = 1;
$d_neuron_death_phenotype = 1;
$d_oxidized_PARK7_dimer_complex = 1;
$d_ubiquitin_phosphorylated = 1;
$nb_mutable = 0;
$u_ATG13_phosphorylated = 1;
$u_ATXN3 = 1;
$u_BAG2 = 1;
$u_BAG4 = 1;
$u_BAG5 = 1;
$u_BCL2L1_BAX_PARK7_complex = 1;
$u_BCL2L1_BAX_complex = 1;
$u_BNIP3L = 1;
$u_CCCP = 1;
$u_DNM1L = 1;
$u_FBXO7 = 1;
$u_FBXW7 = 1;
$u_GABARAP = 1;
$u_GABARAPL1_mitochondrion = 1;
$u_GABARAPL1_neuron = 1;
$u_HSP90 = 1;
$u_HSPA1L = 1;
$u_HSPA9 = 1;
$u_MAP1LC3A_mitochondrion = 1;
$u_MAP1LC3A_neuron = 1;
$u_MARK2 = 1;
$u_NEDD8 = 1;
$u_OPTN = 1;
$u_PARK7_mitochondrion = 1;
$u_PARK7_neuron = 1;
$u_PARL = 1;
$u_PGAM5 = 1;
$u_PGAM5_S = 1;
$u_PINK1 = 1;
$u_PINK1_PRKN_complex_mitochondrion = 1;
$u_PINK1_mitochondrion = 1;
$u_PINK1_neuron = 1;
$u_PMPCA = 1;
$u_PMPCB = 1;
$u_PRKN = 1;
$u_PRKN_ubiquitinated = 1;
$u_ROS = 1;
$u_SIAH3 = 1;
$u_SNCA_mitochondrion = 1;
$u_SNCA_neuron = 1;
$u_SREBF1 = 1;
$u_TIM_Complex_complex = 1;
$u_TOMM20_ubiquitinated = 1;
$u_TOMM40_ubiquitinated = 1;
$u_TOMM70 = 1;
$u_TOM_complex_complex = 1;
$u_VPS13C = 1;
$u_cholesterol = 1;
$u_fatty_acid = 1;
$u_mitochondrial_depolarization_phenotype = 1;
$u_mitophagy_phenotype = 1;
$u_neuron_death_phenotype = 1;
$u_oxidized_PARK7_dimer_complex = 1;
$u_ubiquitin_phosphorylated = 1;
---------------------------------------------------------------------------------------------------------

