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

Run start time: Wed Oct 19 12:37:40 2022
Run end time: Wed Oct 19 12:37:40 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: 6741

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

------------------------------------------------ Network ------------------------------------------------
node UBE2N_UBE2V1_complex {
  rate_up = 0;
  rate_down = $u_UBE2N_UBE2V1_complex;
}

node autophagy_lysosome_system_phenotype {
  rate_up = 0;
  rate_down = $u_autophagy_lysosome_system_phenotype;
}

node GSK3B {
  rate_up = 0;
  rate_down = $u_GSK3B;
}

node excitotoxicity_phenotype {
  rate_up = 0;
  rate_down = $u_excitotoxicity_phenotype;
}

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

node cytosolic_calcium_ion_homeostasis_phenotype {
  rate_up = 0;
  rate_down = $u_cytosolic_calcium_ion_homeostasis_phenotype;
}

node PARP1 {
  logic = (((((NOT excitotoxicity_phenotype AND NOT ROS) AND PARP1)) OR ((NOT excitotoxicity_phenotype AND ROS))) OR (excitotoxicity_phenotype));
  rate_up = (@logic ? $u_PARP1 : 0);
  rate_down = (@logic ? 0 : $d_PARP1);
}

node STK11_acetylated {
  rate_up = 0;
  rate_down = $u_STK11_acetylated;
}

node glycolysis_phenotype {
  logic = (AMPK_complex_neuron);
  rate_up = (@logic ? $u_glycolysis_phenotype : 0);
  rate_down = (@logic ? 0 : $d_glycolysis_phenotype);
}

node ATP {
  logic = (glycolysis_phenotype);
  rate_up = (@logic ? $u_ATP : 0);
  rate_down = (@logic ? 0 : $d_ATP);
}

node AMP {
  logic = (NOT glycolysis_phenotype);
  rate_up = (@logic ? $u_AMP : 0);
  rate_down = (@logic ? 0 : $d_AMP);
}

node NAMPT {
  rate_up = 0;
  rate_down = $u_NAMPT;
}

node nicotinamide {
  logic = (((((((NOT PARP1 AND NOT STK11_acetylated) AND NOT NAD) AND SIRT1)) OR (((NOT PARP1 AND NOT STK11_acetylated) AND NAD))) OR ((NOT PARP1 AND STK11_acetylated))) OR (PARP1));
  rate_up = (@logic ? $u_nicotinamide : 0);
  rate_down = (@logic ? 0 : $d_nicotinamide);
}

node NAD_depletion_phenotype {
  logic = (nicotinamide);
  rate_up = (@logic ? $u_NAD_depletion_phenotype : 0);
  rate_down = (@logic ? 0 : $d_NAD_depletion_phenotype);
}

node NMRK1 {
  rate_up = 0;
  rate_down = $u_NMRK1;
}

node nicotinamide_riboside_NR {
  rate_up = 0;
  rate_down = $u_nicotinamide_riboside_NR;
}

node NAD {
  logic = (((((((NOT NAMPT AND NOT NMRK1) AND NOT nicotinamide_riboside_NR) AND nicotinamide)) OR (((NOT NAMPT AND NOT NMRK1) AND nicotinamide_riboside_NR))) OR ((NOT NAMPT AND NMRK1))) OR (NAMPT));
  rate_up = (@logic ? $u_NAD : 0);
  rate_down = (@logic ? 0 : $d_NAD);
}

node SIRT1 {
  logic = ((((NOT nicotinamide) OR ((((nicotinamide AND NOT NAD) AND NOT caloric_restriction_phenotype) AND resveratrol_drug))) OR (((nicotinamide AND NOT NAD) AND caloric_restriction_phenotype))) OR ((nicotinamide AND NAD)));
  rate_up = (@logic ? $u_SIRT1 : 0);
  rate_down = (@logic ? 0 : $d_SIRT1);
}

node amino_acids_neuron {
  logic = (amino_acids_lysosome);
  rate_up = (@logic ? $u_amino_acids_neuron : 0);
  rate_down = (@logic ? 0 : $d_amino_acids_neuron);
}

node leucine {
  logic = (amino_acids_neuron);
  rate_up = (@logic ? $u_leucine : 0);
  rate_down = (@logic ? 0 : $d_leucine);
}

node PRKN_neuron {
  rate_up = 0;
  rate_down = $u_PRKN_neuron;
}

node energy_homeostasis_phenotype {
  rate_up = 0;
  rate_down = $u_energy_homeostasis_phenotype;
}

node caloric_restriction_phenotype {
  rate_up = 0;
  rate_down = $u_caloric_restriction_phenotype;
}

node GHRL {
  rate_up = 0;
  rate_down = $u_GHRL;
}

node resveratrol_drug {
  rate_up = 0;
  rate_down = $u_resveratrol_drug;
}

node STK11 {
  logic = ((((((NOT STK11_acetylated AND NOT ATP)) OR (((((NOT STK11_acetylated AND ATP) AND NOT AMP) AND NOT NAD) AND SIRT1))) OR ((((NOT STK11_acetylated AND ATP) AND NOT AMP) AND NAD))) OR (((NOT STK11_acetylated AND ATP) AND AMP))) OR (STK11_acetylated));
  rate_up = (@logic ? $u_STK11 : 0);
  rate_down = (@logic ? 0 : $d_STK11);
}

node amino_acids_lysosome {
  logic = (autophagy_lysosome_system_phenotype);
  rate_up = (@logic ? $u_amino_acids_lysosome : 0);
  rate_down = (@logic ? 0 : $d_amino_acids_lysosome);
}

node arginine {
  logic = (amino_acids_lysosome);
  rate_up = (@logic ? $u_arginine : 0);
  rate_down = (@logic ? 0 : $d_arginine);
}

node v_ATPase_complex {
  logic = (amino_acids_lysosome);
  rate_up = (@logic ? $u_v_ATPase_complex : 0);
  rate_down = (@logic ? 0 : $d_v_ATPase_complex);
}

node Ca2_ion {
  logic = (cytosolic_calcium_ion_homeostasis_phenotype);
  rate_up = (@logic ? $u_Ca2_ion : 0);
  rate_down = (@logic ? 0 : $d_Ca2_ion);
}

node Calmodulin_complex {
  logic = (Ca2_ion);
  rate_up = (@logic ? $u_Calmodulin_complex : 0);
  rate_down = (@logic ? 0 : $d_Calmodulin_complex);
}

node CAMKK2 {
  logic = (Calmodulin_complex);
  rate_up = (@logic ? $u_CAMKK2 : 0);
  rate_down = (@logic ? 0 : $d_CAMKK2);
}

node SESN2 {
  logic = (((NOT leucine AND SESN2)) OR (leucine));
  rate_up = (@logic ? $u_SESN2 : 0);
  rate_down = (@logic ? 0 : $d_SESN2);
}

node MAPK1_phosphorylated_phosphorylated {
  rate_up = 0;
  rate_down = $u_MAPK1_phosphorylated_phosphorylated;
}

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

node GATOR2_complex {
  rate_up = 0;
  rate_down = $u_GATOR2_complex;
}

node GATOR1_complex {
  logic = (NOT GATOR2_complex);
  rate_up = (@logic ? $u_GATOR1_complex : 0);
  rate_down = (@logic ? 0 : $d_GATOR1_complex);
}

node Ragulator_SLC38A9_complex {
  logic = (((NOT arginine AND v_ATPase_complex)) OR (arginine));
  rate_up = (@logic ? $u_Ragulator_SLC38A9_complex : 0);
  rate_down = (@logic ? 0 : $d_Ragulator_SLC38A9_complex);
}

node DDB1_CUL4A_complex {
  rate_up = 0;
  rate_down = $u_DDB1_CUL4A_complex;
}

node UCHL1_neuron {
  logic = (((NOT UBE2N_UBE2V1_complex AND UCHL1_PRKN_complex)) OR (UBE2N_UBE2V1_complex));
  rate_up = (@logic ? $u_UCHL1_neuron : 0);
  rate_down = (@logic ? 0 : $d_UCHL1_neuron);
}

node PHLPP1 {
  logic = (NOT UCHL1_neuron);
  rate_up = (@logic ? $u_PHLPP1 : 0);
  rate_down = (@logic ? 0 : $d_PHLPP1);
}

node UCHL1_PRKN_complex {
  rate_up = $u_UCHL1_PRKN_complex;
  rate_down = 0;
}

node mTORC1_complex {
  logic = ((((((NOT Ragulator_SLC38A9_complex AND NOT DDB1_CUL4A_complex) AND NOT UCHL1_neuron)) OR ((((NOT Ragulator_SLC38A9_complex AND NOT DDB1_CUL4A_complex) AND UCHL1_neuron) AND RHEB_lysosome))) OR ((NOT Ragulator_SLC38A9_complex AND DDB1_CUL4A_complex))) OR (Ragulator_SLC38A9_complex));
  rate_up = (@logic ? $u_mTORC1_complex : 0);
  rate_down = (@logic ? 0 : $d_mTORC1_complex);
}

node RPS6KB1_phosphorylated {
  logic = (mTORC1_complex);
  rate_up = (@logic ? $u_RPS6KB1_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_RPS6KB1_phosphorylated);
}

node RHEB_lysosome {
  logic = (((NOT RHEB_lysosome AND TSC1_TSC2_complex_neuron)) OR (RHEB_lysosome));
  rate_up = (@logic ? $u_RHEB_lysosome : 0);
  rate_down = (@logic ? 0 : $d_RHEB_lysosome);
}

node DDIT4 {
  rate_up = 0;
  rate_down = $u_DDIT4;
}

node AMPK_complex_neuron {
  logic = (((((((((((((NOT energy_homeostasis_phenotype AND NOT caloric_restriction_phenotype) AND NOT GHRL) AND NOT resveratrol_drug) AND NOT STK11) AND NOT CAMKK2) AND SESN2)) OR ((((((NOT energy_homeostasis_phenotype AND NOT caloric_restriction_phenotype) AND NOT GHRL) AND NOT resveratrol_drug) AND NOT STK11) AND CAMKK2))) OR (((((NOT energy_homeostasis_phenotype AND NOT caloric_restriction_phenotype) AND NOT GHRL) AND NOT resveratrol_drug) AND STK11))) OR ((((NOT energy_homeostasis_phenotype AND NOT caloric_restriction_phenotype) AND NOT GHRL) AND resveratrol_drug))) OR (((NOT energy_homeostasis_phenotype AND NOT caloric_restriction_phenotype) AND GHRL))) OR ((NOT energy_homeostasis_phenotype AND caloric_restriction_phenotype))) OR (energy_homeostasis_phenotype));
  rate_up = (@logic ? $u_AMPK_complex_neuron : 0);
  rate_down = (@logic ? 0 : $d_AMPK_complex_neuron);
}

node TSC1_TSC2_complex_neuron {
  logic = (((((((((NOT MAPK1_phosphorylated_phosphorylated AND NOT AKT1_phosphorylated) AND NOT DDIT4) AND NOT AMPK_complex_neuron) AND TSC1_TSC2_complex_neuron)) OR ((((NOT MAPK1_phosphorylated_phosphorylated AND NOT AKT1_phosphorylated) AND NOT DDIT4) AND AMPK_complex_neuron))) OR (((NOT MAPK1_phosphorylated_phosphorylated AND NOT AKT1_phosphorylated) AND DDIT4))) OR ((NOT MAPK1_phosphorylated_phosphorylated AND AKT1_phosphorylated))) OR (MAPK1_phosphorylated_phosphorylated));
  rate_up = (@logic ? $u_TSC1_TSC2_complex_neuron : 0);
  rate_down = (@logic ? 0 : $d_TSC1_TSC2_complex_neuron);
}

node mTORC2_complex {
  logic = ((((NOT UCHL1_neuron AND NOT RPS6KB1_phosphorylated)) OR (((NOT UCHL1_neuron AND RPS6KB1_phosphorylated) AND TSC1_TSC2_complex_neuron))) OR (UCHL1_neuron));
  rate_up = (@logic ? $u_mTORC2_complex : 0);
  rate_down = (@logic ? 0 : $d_mTORC2_complex);
}

node DDIT4_phosphorylated {
  logic = (((NOT GSK3B AND DDIT4)) OR (GSK3B));
  rate_up = (@logic ? $u_DDIT4_phosphorylated : 0);
  rate_down = (@logic ? 0 : $d_DDIT4_phosphorylated);
}

node O_acetyl_ADP_D_ribose {
  logic = (((((NOT STK11_acetylated AND NOT NAD) AND SIRT1)) OR ((NOT STK11_acetylated AND NAD))) OR (STK11_acetylated));
  rate_up = (@logic ? $u_O_acetyl_ADP_D_ribose : 0);
  rate_down = (@logic ? 0 : $d_O_acetyl_ADP_D_ribose);
}

node apoptosis_phenotype {
  logic = (NAD_depletion_phenotype);
  rate_up = (@logic ? $u_apoptosis_phenotype : 0);
  rate_down = (@logic ? 0 : $d_apoptosis_phenotype);
}

node parthanatos_phenotype {
  logic = (NAD_depletion_phenotype);
  rate_up = (@logic ? $u_parthanatos_phenotype : 0);
  rate_down = (@logic ? 0 : $d_parthanatos_phenotype);
}

node mitochondrial_dysfunction_phenotype {
  logic = (NAD_depletion_phenotype);
  rate_up = (@logic ? $u_mitochondrial_dysfunction_phenotype : 0);
  rate_down = (@logic ? 0 : $d_mitochondrial_dysfunction_phenotype);
}

node aging_phenotype {
  logic = (NOT nicotinamide_riboside_NR);
  rate_up = (@logic ? $u_aging_phenotype : 0);
  rate_down = (@logic ? 0 : $d_aging_phenotype);
}

node sestrin_GATOR2_complex {
  logic = (((NOT SESN2 AND GATOR2_complex)) OR (SESN2));
  rate_up = (@logic ? $u_sestrin_GATOR2_complex : 0);
  rate_down = (@logic ? 0 : $d_sestrin_GATOR2_complex);
}

node epilepsy_familial_focal_phenotype {
  logic = (GATOR1_complex);
  rate_up = (@logic ? $u_epilepsy_familial_focal_phenotype : 0);
  rate_down = (@logic ? 0 : $d_epilepsy_familial_focal_phenotype);
}

node Akt_pathway_phenotype {
  logic = ((NOT PHLPP1) OR ((PHLPP1 AND mTORC2_complex)));
  rate_up = (@logic ? $u_Akt_pathway_phenotype : 0);
  rate_down = (@logic ? 0 : $d_Akt_pathway_phenotype);
}

node catabolism_phenotype {
  logic = (AMPK_complex_neuron);
  rate_up = (@logic ? $u_catabolism_phenotype : 0);
  rate_down = (@logic ? 0 : $d_catabolism_phenotype);
}
---------------------------------------------------------------------------------------------------------

----------------------------------------------- Variables -----------------------------------------------
$d_AKT1_phosphorylated = 1;
$d_AMP = 1;
$d_AMPK_complex_neuron = 1;
$d_ATP = 1;
$d_Akt_pathway_phenotype = 1;
$d_CAMKK2 = 1;
$d_Ca2_ion = 1;
$d_Calmodulin_complex = 1;
$d_DDB1_CUL4A_complex = 1;
$d_DDIT4 = 1;
$d_DDIT4_phosphorylated = 1;
$d_GATOR1_complex = 1;
$d_GATOR2_complex = 1;
$d_GHRL = 1;
$d_GSK3B = 1;
$d_MAPK1_phosphorylated_phosphorylated = 1;
$d_NAD = 1;
$d_NAD_depletion_phenotype = 1;
$d_NAMPT = 1;
$d_NMRK1 = 1;
$d_O_acetyl_ADP_D_ribose = 1;
$d_PARP1 = 1;
$d_PHLPP1 = 1;
$d_PRKN_neuron = 1;
$d_RHEB_lysosome = 1;
$d_ROS = 1;
$d_RPS6KB1_phosphorylated = 1;
$d_Ragulator_SLC38A9_complex = 1;
$d_SESN2 = 1;
$d_SIRT1 = 1;
$d_STK11 = 1;
$d_STK11_acetylated = 1;
$d_TSC1_TSC2_complex_neuron = 1;
$d_UBE2N_UBE2V1_complex = 1;
$d_UCHL1_PRKN_complex = 1;
$d_UCHL1_neuron = 1;
$d_aging_phenotype = 1;
$d_amino_acids_lysosome = 1;
$d_amino_acids_neuron = 1;
$d_apoptosis_phenotype = 1;
$d_arginine = 1;
$d_autophagy_lysosome_system_phenotype = 1;
$d_caloric_restriction_phenotype = 1;
$d_catabolism_phenotype = 1;
$d_cytosolic_calcium_ion_homeostasis_phenotype = 1;
$d_energy_homeostasis_phenotype = 1;
$d_epilepsy_familial_focal_phenotype = 1;
$d_excitotoxicity_phenotype = 1;
$d_glycolysis_phenotype = 1;
$d_leucine = 1;
$d_mTORC1_complex = 1;
$d_mTORC2_complex = 1;
$d_mitochondrial_dysfunction_phenotype = 1;
$d_nicotinamide = 1;
$d_nicotinamide_riboside_NR = 1;
$d_parthanatos_phenotype = 1;
$d_resveratrol_drug = 1;
$d_sestrin_GATOR2_complex = 1;
$d_v_ATPase_complex = 1;
$nb_mutable = 0;
$u_AKT1_phosphorylated = 1;
$u_AMP = 1;
$u_AMPK_complex_neuron = 1;
$u_ATP = 1;
$u_Akt_pathway_phenotype = 1;
$u_CAMKK2 = 1;
$u_Ca2_ion = 1;
$u_Calmodulin_complex = 1;
$u_DDB1_CUL4A_complex = 1;
$u_DDIT4 = 1;
$u_DDIT4_phosphorylated = 1;
$u_GATOR1_complex = 1;
$u_GATOR2_complex = 1;
$u_GHRL = 1;
$u_GSK3B = 1;
$u_MAPK1_phosphorylated_phosphorylated = 1;
$u_NAD = 1;
$u_NAD_depletion_phenotype = 1;
$u_NAMPT = 1;
$u_NMRK1 = 1;
$u_O_acetyl_ADP_D_ribose = 1;
$u_PARP1 = 1;
$u_PHLPP1 = 1;
$u_PRKN_neuron = 1;
$u_RHEB_lysosome = 1;
$u_ROS = 1;
$u_RPS6KB1_phosphorylated = 1;
$u_Ragulator_SLC38A9_complex = 1;
$u_SESN2 = 1;
$u_SIRT1 = 1;
$u_STK11 = 1;
$u_STK11_acetylated = 1;
$u_TSC1_TSC2_complex_neuron = 1;
$u_UBE2N_UBE2V1_complex = 1;
$u_UCHL1_PRKN_complex = 1;
$u_UCHL1_neuron = 1;
$u_aging_phenotype = 1;
$u_amino_acids_lysosome = 1;
$u_amino_acids_neuron = 1;
$u_apoptosis_phenotype = 1;
$u_arginine = 1;
$u_autophagy_lysosome_system_phenotype = 1;
$u_caloric_restriction_phenotype = 1;
$u_catabolism_phenotype = 1;
$u_cytosolic_calcium_ion_homeostasis_phenotype = 1;
$u_energy_homeostasis_phenotype = 1;
$u_epilepsy_familial_focal_phenotype = 1;
$u_excitotoxicity_phenotype = 1;
$u_glycolysis_phenotype = 1;
$u_leucine = 1;
$u_mTORC1_complex = 1;
$u_mTORC2_complex = 1;
$u_mitochondrial_dysfunction_phenotype = 1;
$u_nicotinamide = 1;
$u_nicotinamide_riboside_NR = 1;
$u_parthanatos_phenotype = 1;
$u_resveratrol_drug = 1;
$u_sestrin_GATOR2_complex = 1;
$u_v_ATPase_complex = 1;
---------------------------------------------------------------------------------------------------------

