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

Run start time: Sun Nov  6 17:04:59 2022
Run end time: Sun Nov  6 17:04:59 2022

Core user runtime: 0.02 secs using 6 threads
Core elapsed runtime: 0.01 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: 6681

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

------------------------------------------------ Network ------------------------------------------------
node FZD1_neuron {
  rate_up = 0;
  rate_down = $u_FZD1_neuron;
}

node WNT3 {
  rate_up = 0;
  rate_down = $u_WNT3;
}

node WNT_signalosome_complex {
  logic = (((NOT FZD1_neuron AND WNT3)) OR (FZD1_neuron));
  rate_up = (@logic ? $u_WNT_signalosome_complex : 0);
  rate_down = (@logic ? 0 : $d_WNT_signalosome_complex);
}

node WNT1 {
  rate_up = 0;
  rate_down = $u_WNT1;
}

node FZD1_WNT1_complex {
  logic = (((NOT FZD1_neuron AND WNT1)) OR (FZD1_neuron));
  rate_up = (@logic ? $u_FZD1_WNT1_complex : 0);
  rate_down = (@logic ? 0 : $d_FZD1_WNT1_complex);
}

node CTNNB1 {
  logic = (FZD1_WNT1_complex);
  rate_up = (@logic ? $u_CTNNB1 : 0);
  rate_down = (@logic ? 0 : $d_CTNNB1);
}

node PRKCD {
  rate_up = 0;
  rate_down = $u_PRKCD;
}

node TFEB_phosphorylated {
  logic = (NOT GSK3B);
  rate_up = (@logic ? $u_TFEB_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_TFEB_phosphorylated);
}

node GSK3B {
  logic = (NOT TFEB_phosphorylated);
  rate_up = (@logic ? $u_GSK3B : 0);
  rate_down = (@logic ? 0 : $d_GSK3B);
}

node mTORC1_complex_neuron {
  rate_up = $u_mTORC1_complex_neuron;
  rate_down = 0;
}

node MAPK1 {
  rate_up = 0;
  rate_down = $u_MAPK1;
}

node CTNNB1_phosphorylated {
  rate_up = $u_CTNNB1_phosphorylated;
  rate_down = 0;
}

node GDNF_rna {
  rate_up = 0;
  rate_down = $u_GDNF_rna;
}

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

node EIF2AK3 {
  rate_up = 0;
  rate_down = $u_EIF2AK3;
}

node EIF2A_phosphorylated {
  rate_up = 0;
  rate_down = $u_EIF2A_phosphorylated;
}

node TFDP1 {
  rate_up = 0;
  rate_down = $u_TFDP1;
}

node LRRK2_neuron {
  logic = (LRRK2_neuron);
  rate_up = (@logic ? $u_LRRK2_neuron : 0);
  rate_down = (@logic ? 0 : $d_LRRK2_neuron);
}

node RPS15_phosphorylated {
  logic = (LRRK2_neuron);
  rate_up = (@logic ? $u_RPS15_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_RPS15_phosphorylated);
}

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

node protofibril_complex {
  logic = (SNCA);
  rate_up = (@logic ? $u_protofibril_complex : 0);
  rate_down = (@logic ? 0 : $d_protofibril_complex);
}

node PP2A_complex {
  logic = (NOT protofibril_complex);
  rate_up = (@logic ? $u_PP2A_complex : 0);
  rate_down = (@logic ? 0 : $d_PP2A_complex);
}

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

node autophagy_phenotype {
  logic = (((TFEB_phosphorylated AND LRRK2_neuron) AND TFEB_SNCA_complex));
  rate_up = (@logic ? $u_autophagy_phenotype : 0);
  rate_down = (@logic ? 0 : $d_autophagy_phenotype);
}

node amino_acid {
  logic = (autophagy_phenotype);
  rate_up = (@logic ? $u_amino_acid : 0);
  rate_down = (@logic ? 0 : $d_amino_acid);
}

node AKT1 {
  rate_up = $u_AKT1;
  rate_down = 0;
}

node Akt_pathway_phenotype {
  logic = (NOT SNCA);
  rate_up = (@logic ? $u_Akt_pathway_phenotype : 0);
  rate_down = (@logic ? 0 : $d_Akt_pathway_phenotype);
}

node mTORC2_complex {
  rate_up = $u_mTORC2_complex;
  rate_down = 0;
}

node TFEB_SNCA_complex {
  logic = (((NOT TFEB_phosphorylated AND SNCA)) OR (TFEB_phosphorylated));
  rate_up = (@logic ? $u_TFEB_SNCA_complex : 0);
  rate_down = (@logic ? 0 : $d_TFEB_SNCA_complex);
}

node RPS6KB1_phosphorylated {
  logic = (((NOT mTORC1_complex_neuron AND NOT PP2A_complex)) OR (mTORC1_complex_neuron));
  rate_up = (@logic ? $u_RPS6KB1_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_RPS6KB1_phosphorylated);
}

node EIF4E {
  rate_up = 0;
  rate_down = $u_EIF4E;
}

node translation_phenotype {
  logic = (((((NOT EIF2A_phosphorylated) OR (((((EIF2A_phosphorylated AND NOT TFDP1) AND NOT RPS15_phosphorylated) AND NOT RPS6KB1_phosphorylated) AND EIF4E))) OR ((((EIF2A_phosphorylated AND NOT TFDP1) AND NOT RPS15_phosphorylated) AND RPS6KB1_phosphorylated))) OR (((EIF2A_phosphorylated AND NOT TFDP1) AND RPS15_phosphorylated))) OR ((EIF2A_phosphorylated AND TFDP1)));
  rate_up = (@logic ? $u_translation_phenotype : 0);
  rate_down = (@logic ? 0 : $d_translation_phenotype);
}

node IGF1 {
  rate_up = 0;
  rate_down = $u_IGF1;
}

node ROS_default_compartment {
  rate_up = 0;
  rate_down = $u_ROS_default_compartment;
}

node NEDD4 {
  rate_up = 0;
  rate_down = $u_NEDD4;
}

node IGF1R {
  logic = ((((NOT IGF1 AND NOT ROS_default_compartment)) OR (((NOT IGF1 AND ROS_default_compartment) AND NOT NEDD4))) OR (IGF1));
  rate_up = (@logic ? $u_IGF1R : 0);
  rate_down = (@logic ? 0 : $d_IGF1R);
}

node PHLPP1 {
  rate_up = 0;
  rate_down = $u_PHLPP1;
}

node IRS1_phosphorylated {
  logic = ((((((((NOT protofibril_complex AND NOT PP2A_complex)) OR (((((((NOT protofibril_complex AND PP2A_complex) AND NOT RPS6KB1_phosphorylated) AND NOT IGF1R) AND NOT IRS1_phosphorylated) AND NOT MAPK14_phosphorylated) AND INSR_INS_complex_neuron))) OR ((((((NOT protofibril_complex AND PP2A_complex) AND NOT RPS6KB1_phosphorylated) AND NOT IGF1R) AND NOT IRS1_phosphorylated) AND MAPK14_phosphorylated))) OR (((((NOT protofibril_complex AND PP2A_complex) AND NOT RPS6KB1_phosphorylated) AND NOT IGF1R) AND IRS1_phosphorylated))) OR ((((NOT protofibril_complex AND PP2A_complex) AND NOT RPS6KB1_phosphorylated) AND IGF1R))) OR (((NOT protofibril_complex AND PP2A_complex) AND RPS6KB1_phosphorylated))) OR (protofibril_complex));
  rate_up = (@logic ? $u_IRS1_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_IRS1_phosphorylated);
}

node MAPK14_phosphorylated {
  rate_up = 0;
  rate_down = $u_MAPK14_phosphorylated;
}

node INSR_INS_complex_neuron {
  logic = (INSR);
  rate_up = (@logic ? $u_INSR_INS_complex_neuron : 0);
  rate_down = (@logic ? 0 : $d_INSR_INS_complex_neuron);
}

node PTEN {
  rate_up = 0;
  rate_down = $u_PTEN;
}

node CCN4 {
  rate_up = 0;
  rate_down = $u_CCN4;
}

node PI3K_cascade_phenotype {
  logic = ((((NOT IRS1_phosphorylated AND NOT PTEN)) OR (((NOT IRS1_phosphorylated AND PTEN) AND CCN4))) OR (IRS1_phosphorylated));
  rate_up = (@logic ? $u_PI3K_cascade_phenotype : 0);
  rate_down = (@logic ? 0 : $d_PI3K_cascade_phenotype);
}

node RET {
  rate_up = 0;
  rate_down = $u_RET;
}

node GFRA1_GDNF_complex {
  rate_up = 0;
  rate_down = $u_GFRA1_GDNF_complex;
}

node INSR {
  logic = (INSR_INS_complex_endocytic_vesicle);
  rate_up = (@logic ? $u_INSR : 0);
  rate_down = (@logic ? 0 : $d_INSR);
}

node INSR_INS_complex_endocytic_vesicle {
  logic = (INSR_INS_complex_neuron);
  rate_up = (@logic ? $u_INSR_INS_complex_endocytic_vesicle : 0);
  rate_down = (@logic ? 0 : $d_INSR_INS_complex_endocytic_vesicle);
}

node NTRK1 {
  rate_up = 0;
  rate_down = $u_NTRK1;
}

node insulin_resistence {
  logic = (IGF1R);
  rate_up = (@logic ? $u_insulin_resistence : 0);
  rate_down = (@logic ? 0 : $d_insulin_resistence);
}

node EIF4EBP1 {
  rate_up = 0;
  rate_down = $u_EIF4EBP1;
}

node EIF4EBP1_phosphorylated {
  logic = (((((NOT mTORC1_complex_neuron AND NOT LRRK2_neuron) AND EIF4EBP1)) OR ((NOT mTORC1_complex_neuron AND LRRK2_neuron))) OR (mTORC1_complex_neuron));
  rate_up = (@logic ? $u_EIF4EBP1_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_EIF4EBP1_phosphorylated);
}

node AGO2 {
  rate_up = 0;
  rate_down = $u_AGO2;
}

node IDE_SNCA_protofibril_complex {
  logic = (protofibril_complex);
  rate_up = (@logic ? $u_IDE_SNCA_protofibril_complex : 0);
  rate_down = (@logic ? 0 : $d_IDE_SNCA_protofibril_complex);
}

node GSK3B_phosphorylated {
  logic = (((NOT WNT_signalosome_complex AND GSK3B)) OR (WNT_signalosome_complex));
  rate_up = (@logic ? $u_GSK3B_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_GSK3B_phosphorylated);
}

node CTNNB1_ubiquitinated_phosphorylated {
  logic = (((NOT CTNNB1_phosphorylated AND PRKN)) OR (CTNNB1_phosphorylated));
  rate_up = (@logic ? $u_CTNNB1_ubiquitinated_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_CTNNB1_ubiquitinated_phosphorylated);
}

node catenin_import_into_nucleus_phenotype {
  logic = (CTNNB1);
  rate_up = (@logic ? $u_catenin_import_into_nucleus_phenotype : 0);
  rate_down = (@logic ? 0 : $d_catenin_import_into_nucleus_phenotype);
}

node TFEB_complex {
  logic = (((NOT GSK3B AND TFEB_phosphorylated)) OR (GSK3B));
  rate_up = (@logic ? $u_TFEB_complex : 0);
  rate_down = (@logic ? 0 : $d_TFEB_complex);
}

node EIF4EBP1_EIF4E_complex {
  logic = (((NOT EIF4E AND EIF4EBP1)) OR (EIF4E));
  rate_up = (@logic ? $u_EIF4EBP1_EIF4E_complex : 0);
  rate_down = (@logic ? 0 : $d_EIF4EBP1_EIF4E_complex);
}

node neuron_death_phenotype {
  logic = (NOT EIF4EBP1_EIF4E_complex);
  rate_up = (@logic ? $u_neuron_death_phenotype : 0);
  rate_down = (@logic ? 0 : $d_neuron_death_phenotype);
}

node EBP1_AGO2_complex {
  logic = (((((NOT LRRK2_neuron AND NOT EIF4EBP1_phosphorylated) AND AGO2)) OR ((NOT LRRK2_neuron AND EIF4EBP1_phosphorylated))) OR (LRRK2_neuron));
  rate_up = (@logic ? $u_EBP1_AGO2_complex : 0);
  rate_down = (@logic ? 0 : $d_EBP1_AGO2_complex);
}
---------------------------------------------------------------------------------------------------------

----------------------------------------------- Variables -----------------------------------------------
$d_AGO2 = 1;
$d_AKT1 = 1;
$d_AKT1_phosphorylated = 1;
$d_Akt_pathway_phenotype = 1;
$d_CCN4 = 1;
$d_CTNNB1 = 1;
$d_CTNNB1_phosphorylated = 1;
$d_CTNNB1_ubiquitinated_phosphorylated = 1;
$d_EBP1_AGO2_complex = 1;
$d_EIF2AK3 = 1;
$d_EIF2A_phosphorylated = 1;
$d_EIF4E = 1;
$d_EIF4EBP1 = 1;
$d_EIF4EBP1_EIF4E_complex = 1;
$d_EIF4EBP1_phosphorylated = 1;
$d_FZD1_WNT1_complex = 1;
$d_FZD1_neuron = 1;
$d_GDNF_rna = 1;
$d_GFRA1_GDNF_complex = 1;
$d_GSK3B = 1;
$d_GSK3B_phosphorylated = 1;
$d_IDE_SNCA_protofibril_complex = 1;
$d_IGF1 = 1;
$d_IGF1R = 1;
$d_INSR = 1;
$d_INSR_INS_complex_endocytic_vesicle = 1;
$d_INSR_INS_complex_neuron = 1;
$d_IRS1_phosphorylated = 1;
$d_LRRK2_neuron = 1;
$d_MAPK1 = 1;
$d_MAPK14_phosphorylated = 1;
$d_NEDD4 = 1;
$d_NTRK1 = 1;
$d_PHLPP1 = 1;
$d_PI3K_cascade_phenotype = 1;
$d_PP2A_complex = 1;
$d_PRKCD = 1;
$d_PRKN = 1;
$d_PTEN = 1;
$d_RET = 1;
$d_ROS_default_compartment = 1;
$d_RPS15_phosphorylated = 1;
$d_RPS6KB1_phosphorylated = 1;
$d_SNCA = 1;
$d_TFDP1 = 1;
$d_TFEB_SNCA_complex = 1;
$d_TFEB_complex = 1;
$d_TFEB_phosphorylated = 1;
$d_WNT1 = 1;
$d_WNT3 = 1;
$d_WNT_signalosome_complex = 1;
$d_amino_acid = 1;
$d_autophagy_phenotype = 1;
$d_catenin_import_into_nucleus_phenotype = 1;
$d_insulin_resistence = 1;
$d_mTORC1_complex_neuron = 1;
$d_mTORC2_complex = 1;
$d_neuron_death_phenotype = 1;
$d_protofibril_complex = 1;
$d_translation_phenotype = 1;
$nb_mutable = 0;
$u_AGO2 = 1;
$u_AKT1 = 1;
$u_AKT1_phosphorylated = 1;
$u_Akt_pathway_phenotype = 1;
$u_CCN4 = 1;
$u_CTNNB1 = 1;
$u_CTNNB1_phosphorylated = 1;
$u_CTNNB1_ubiquitinated_phosphorylated = 1;
$u_EBP1_AGO2_complex = 1;
$u_EIF2AK3 = 1;
$u_EIF2A_phosphorylated = 1;
$u_EIF4E = 1;
$u_EIF4EBP1 = 1;
$u_EIF4EBP1_EIF4E_complex = 1;
$u_EIF4EBP1_phosphorylated = 1;
$u_FZD1_WNT1_complex = 1;
$u_FZD1_neuron = 1;
$u_GDNF_rna = 1;
$u_GFRA1_GDNF_complex = 1;
$u_GSK3B = 1;
$u_GSK3B_phosphorylated = 1;
$u_IDE_SNCA_protofibril_complex = 1;
$u_IGF1 = 1;
$u_IGF1R = 1;
$u_INSR = 1;
$u_INSR_INS_complex_endocytic_vesicle = 1;
$u_INSR_INS_complex_neuron = 1;
$u_IRS1_phosphorylated = 1;
$u_LRRK2_neuron = 1;
$u_MAPK1 = 1;
$u_MAPK14_phosphorylated = 1;
$u_NEDD4 = 1;
$u_NTRK1 = 1;
$u_PHLPP1 = 1;
$u_PI3K_cascade_phenotype = 1;
$u_PP2A_complex = 1;
$u_PRKCD = 1;
$u_PRKN = 1;
$u_PTEN = 1;
$u_RET = 1;
$u_ROS_default_compartment = 1;
$u_RPS15_phosphorylated = 1;
$u_RPS6KB1_phosphorylated = 1;
$u_SNCA = 1;
$u_TFDP1 = 1;
$u_TFEB_SNCA_complex = 1;
$u_TFEB_complex = 1;
$u_TFEB_phosphorylated = 1;
$u_WNT1 = 1;
$u_WNT3 = 1;
$u_WNT_signalosome_complex = 1;
$u_amino_acid = 1;
$u_autophagy_phenotype = 1;
$u_catenin_import_into_nucleus_phenotype = 1;
$u_insulin_resistence = 1;
$u_mTORC1_complex_neuron = 1;
$u_mTORC2_complex = 1;
$u_neuron_death_phenotype = 1;
$u_protofibril_complex = 1;
$u_translation_phenotype = 1;
---------------------------------------------------------------------------------------------------------

