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

Run start time: Wed Oct 19 12:26:36 2022
Run end time: Wed Oct 19 12:26:36 2022

Core user runtime: 0.03 secs using 6 threads
Core elapsed runtime: 0.014 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: 9795

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

------------------------------------------------ Network ------------------------------------------------
node PARK7 {
  logic = (PIAS4);
  rate_up = (@logic ? $u_PARK7 : 0);
  rate_down = (@logic ? 0 : $d_PARK7);
}

node SFPQ {
  logic = (NOT PARK7);
  rate_up = (@logic ? $u_SFPQ : 0);
  rate_down = (@logic ? 0 : $d_SFPQ);
}

node retinoic_acid {
  rate_up = 0;
  rate_down = $u_retinoic_acid;
}

node TF_LMX1A_B_complex {
  rate_up = 0;
  rate_down = $u_TF_LMX1A_B_complex;
}

node MAP1B_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_MAP1B_rna : 0);
  rate_down = (@logic ? 0 : $d_MAP1B_rna);
}

node KLC1_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_KLC1_rna : 0);
  rate_down = (@logic ? 0 : $d_KLC1_rna);
}

node DYNC1H1_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_DYNC1H1_rna : 0);
  rate_down = (@logic ? 0 : $d_DYNC1H1_rna);
}

node DCTN1_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_DCTN1_rna : 0);
  rate_down = (@logic ? 0 : $d_DCTN1_rna);
}

node KIF1A_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_KIF1A_rna : 0);
  rate_down = (@logic ? 0 : $d_KIF1A_rna);
}

node TFEB_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_TFEB_rna : 0);
  rate_down = (@logic ? 0 : $d_TFEB_rna);
}

node TF_FOXA1_2_complex {
  rate_up = 0;
  rate_down = $u_TF_FOXA1_2_complex;
}

node RXRA {
  logic = (retinoic_acid);
  rate_up = (@logic ? $u_RXRA : 0);
  rate_down = (@logic ? 0 : $d_RXRA);
}

node FOXA2 {
  rate_up = 0;
  rate_down = $u_FOXA2;
}

node PIN1 {
  rate_up = 0;
  rate_down = $u_PIN1;
}

node PITX3_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_PITX3_rna : 0);
  rate_down = (@logic ? 0 : $d_PITX3_rna);
}

node MIR133B_rna {
  logic = (TF_PITX3_complex);
  rate_up = (@logic ? $u_MIR133B_rna : 0);
  rate_down = (@logic ? 0 : $d_MIR133B_rna);
}

node PITX3 {
  logic = (((NOT PITX3_rna AND NOT MIR133B_rna)) OR (PITX3_rna));
  rate_up = (@logic ? $u_PITX3 : 0);
  rate_down = (@logic ? 0 : $d_PITX3);
}

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

node NCOR2 {
  rate_up = 0;
  rate_down = $u_NCOR2;
}

node PIAS4 {
  rate_up = 0;
  rate_down = $u_PIAS4;
}

node NR4A2_nucleus {
  logic = (((NOT PIAS4 AND NR4A2_nucleus)) OR (PIAS4));
  rate_up = (@logic ? $u_NR4A2_nucleus : 0);
  rate_down = (@logic ? 0 : $d_NR4A2_nucleus);
}

node TF_NR4A2_complex {
  logic = ((((((((((((NOT RXRA AND NOT FOXA2) AND NOT PIN1) AND NOT PITX3) AND NOT SNCA)) OR ((((((NOT RXRA AND NOT FOXA2) AND NOT PIN1) AND NOT PITX3) AND SNCA) AND NOT NCOR2))) OR (((((((NOT RXRA AND NOT FOXA2) AND NOT PIN1) AND NOT PITX3) AND SNCA) AND NCOR2) AND NOT PIAS4))) OR ((((((((NOT RXRA AND NOT FOXA2) AND NOT PIN1) AND NOT PITX3) AND SNCA) AND NCOR2) AND PIAS4) AND NR4A2_nucleus))) OR ((((NOT RXRA AND NOT FOXA2) AND NOT PIN1) AND PITX3))) OR (((NOT RXRA AND NOT FOXA2) AND PIN1))) OR ((NOT RXRA AND FOXA2))) OR (RXRA));
  rate_up = (@logic ? $u_TF_NR4A2_complex : 0);
  rate_down = (@logic ? 0 : $d_TF_NR4A2_complex);
}

node NDUFB8_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_NDUFB8_rna : 0);
  rate_down = (@logic ? 0 : $d_NDUFB8_rna);
}

node GCH1_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_GCH1_rna : 0);
  rate_down = (@logic ? 0 : $d_GCH1_rna);
}

node COX6A1_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_COX6A1_rna : 0);
  rate_down = (@logic ? 0 : $d_COX6A1_rna);
}

node COX5A_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_COX5A_rna : 0);
  rate_down = (@logic ? 0 : $d_COX5A_rna);
}

node COX8A_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_COX8A_rna : 0);
  rate_down = (@logic ? 0 : $d_COX8A_rna);
}

node DDC_rna {
  logic = (((NOT TF_FOXA1_2_complex AND TF_NR4A2_complex)) OR (TF_FOXA1_2_complex));
  rate_up = (@logic ? $u_DDC_rna : 0);
  rate_down = (@logic ? 0 : $d_DDC_rna);
}

node RET_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_RET_rna : 0);
  rate_down = (@logic ? 0 : $d_RET_rna);
}

node COX5B_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_COX5B_rna : 0);
  rate_down = (@logic ? 0 : $d_COX5B_rna);
}

node PBX1 {
  rate_up = 0;
  rate_down = $u_PBX1;
}

node LRRK2 {
  rate_up = 0;
  rate_down = $u_LRRK2;
}

node TF_PITX3_complex {
  logic = (((NOT PBX1 AND NOT LRRK2)) OR (PBX1));
  rate_up = (@logic ? $u_TF_PITX3_complex : 0);
  rate_down = (@logic ? 0 : $d_TF_PITX3_complex);
}

node KCNJ6_rna {
  logic = (TF_PITX3_complex);
  rate_up = (@logic ? $u_KCNJ6_rna : 0);
  rate_down = (@logic ? 0 : $d_KCNJ6_rna);
}

node BDNF_rna {
  logic = (((NOT TF_NR4A2_complex AND TF_PITX3_complex)) OR (TF_NR4A2_complex));
  rate_up = (@logic ? $u_BDNF_rna : 0);
  rate_down = (@logic ? 0 : $d_BDNF_rna);
}

node SLC18A2_rna {
  logic = (((((NOT TF_FOXA1_2_complex AND NOT TF_NR4A2_complex) AND TF_PITX3_complex)) OR ((NOT TF_FOXA1_2_complex AND TF_NR4A2_complex))) OR (TF_FOXA1_2_complex));
  rate_up = (@logic ? $u_SLC18A2_rna : 0);
  rate_down = (@logic ? 0 : $d_SLC18A2_rna);
}

node SLC6A3_rna {
  logic = (((((NOT TF_FOXA1_2_complex AND NOT TF_NR4A2_complex) AND TF_PITX3_complex)) OR ((NOT TF_FOXA1_2_complex AND TF_NR4A2_complex))) OR (TF_FOXA1_2_complex));
  rate_up = (@logic ? $u_SLC6A3_rna : 0);
  rate_down = (@logic ? 0 : $d_SLC6A3_rna);
}

node DRD2_rna {
  logic = (((((NOT TF_FOXA1_2_complex AND NOT TF_NR4A2_complex) AND TF_PITX3_complex)) OR ((NOT TF_FOXA1_2_complex AND TF_NR4A2_complex))) OR (TF_FOXA1_2_complex));
  rate_up = (@logic ? $u_DRD2_rna : 0);
  rate_down = (@logic ? 0 : $d_DRD2_rna);
}

node ALDH1A1_rna {
  logic = (((((NOT TF_FOXA1_2_complex AND NOT TF_NR4A2_complex) AND TF_PITX3_complex)) OR ((NOT TF_FOXA1_2_complex AND TF_NR4A2_complex))) OR (TF_FOXA1_2_complex));
  rate_up = (@logic ? $u_ALDH1A1_rna : 0);
  rate_down = (@logic ? 0 : $d_ALDH1A1_rna);
}

node TH_rna {
  logic = ((((NOT SFPQ) OR ((((SFPQ AND NOT TF_FOXA1_2_complex) AND NOT TF_NR4A2_complex) AND TF_PITX3_complex))) OR (((SFPQ AND NOT TF_FOXA1_2_complex) AND TF_NR4A2_complex))) OR ((SFPQ AND TF_FOXA1_2_complex)));
  rate_up = (@logic ? $u_TH_rna : 0);
  rate_down = (@logic ? 0 : $d_TH_rna);
}

node GDNF_rna {
  logic = (TF_PITX3_complex);
  rate_up = (@logic ? $u_GDNF_rna : 0);
  rate_down = (@logic ? 0 : $d_GDNF_rna);
}

node axonal_transport_phenotype {
  logic = (((((((((NOT MAP1B_rna AND NOT KLC1_rna) AND NOT DYNC1H1_rna) AND NOT DCTN1_rna) AND KIF1A_rna)) OR ((((NOT MAP1B_rna AND NOT KLC1_rna) AND NOT DYNC1H1_rna) AND DCTN1_rna))) OR (((NOT MAP1B_rna AND NOT KLC1_rna) AND DYNC1H1_rna))) OR ((NOT MAP1B_rna AND KLC1_rna))) OR (MAP1B_rna));
  rate_up = (@logic ? $u_axonal_transport_phenotype : 0);
  rate_down = (@logic ? 0 : $d_axonal_transport_phenotype);
}

node NRF1_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_NRF1_rna : 0);
  rate_down = (@logic ? 0 : $d_NRF1_rna);
}

node NR4A2_rna {
  logic = (((NOT TF_LMX1A_B_complex AND TF_FOXA1_2_complex)) OR (TF_LMX1A_B_complex));
  rate_up = (@logic ? $u_NR4A2_rna : 0);
  rate_down = (@logic ? 0 : $d_NR4A2_rna);
}

node FOXO3_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_FOXO3_rna : 0);
  rate_down = (@logic ? 0 : $d_FOXO3_rna);
}

node FOXO1_rna {
  logic = (TF_LMX1A_B_complex);
  rate_up = (@logic ? $u_FOXO1_rna : 0);
  rate_down = (@logic ? 0 : $d_FOXO1_rna);
}

node autophagy_phenotype {
  logic = (TFEB_rna);
  rate_up = (@logic ? $u_autophagy_phenotype : 0);
  rate_down = (@logic ? 0 : $d_autophagy_phenotype);
}

node LMX1B_rna {
  logic = (TF_FOXA1_2_complex);
  rate_up = (@logic ? $u_LMX1B_rna : 0);
  rate_down = (@logic ? 0 : $d_LMX1B_rna);
}

node EN1_rna {
  logic = (TF_FOXA1_2_complex);
  rate_up = (@logic ? $u_EN1_rna : 0);
  rate_down = (@logic ? 0 : $d_EN1_rna);
}

node LMX1A_rna {
  logic = (TF_FOXA1_2_complex);
  rate_up = (@logic ? $u_LMX1A_rna : 0);
  rate_down = (@logic ? 0 : $d_LMX1A_rna);
}

node NKX6_1_rna {
  logic = (TF_FOXA1_2_complex);
  rate_up = (@logic ? $u_NKX6_1_rna : 0);
  rate_down = (@logic ? 0 : $d_NKX6_1_rna);
}

node mitochondrial_biogenesis_phenotype {
  logic = (((((((((NOT NDUFB8_rna AND NOT COX6A1_rna) AND NOT COX5A_rna) AND NOT COX8A_rna) AND COX5B_rna)) OR ((((NOT NDUFB8_rna AND NOT COX6A1_rna) AND NOT COX5A_rna) AND COX8A_rna))) OR (((NOT NDUFB8_rna AND NOT COX6A1_rna) AND COX5A_rna))) OR ((NOT NDUFB8_rna AND COX6A1_rna))) OR (NDUFB8_rna));
  rate_up = (@logic ? $u_mitochondrial_biogenesis_phenotype : 0);
  rate_down = (@logic ? 0 : $d_mitochondrial_biogenesis_phenotype);
}

node dopamine_metabolism_phenotype {
  logic = (((((((((((((NOT GCH1_rna AND NOT DDC_rna) AND NOT SLC18A2_rna) AND NOT SLC6A3_rna) AND NOT DRD2_rna) AND NOT ALDH1A1_rna) AND TH_rna)) OR ((((((NOT GCH1_rna AND NOT DDC_rna) AND NOT SLC18A2_rna) AND NOT SLC6A3_rna) AND NOT DRD2_rna) AND ALDH1A1_rna))) OR (((((NOT GCH1_rna AND NOT DDC_rna) AND NOT SLC18A2_rna) AND NOT SLC6A3_rna) AND DRD2_rna))) OR ((((NOT GCH1_rna AND NOT DDC_rna) AND NOT SLC18A2_rna) AND SLC6A3_rna))) OR (((NOT GCH1_rna AND NOT DDC_rna) AND SLC18A2_rna))) OR ((NOT GCH1_rna AND DDC_rna))) OR (GCH1_rna));
  rate_up = (@logic ? $u_dopamine_metabolism_phenotype : 0);
  rate_down = (@logic ? 0 : $d_dopamine_metabolism_phenotype);
}

node neuron_survival_phenotype {
  logic = (((((NOT RET_rna AND NOT BDNF_rna) AND GDNF_rna)) OR ((NOT RET_rna AND BDNF_rna))) OR (RET_rna));
  rate_up = (@logic ? $u_neuron_survival_phenotype : 0);
  rate_down = (@logic ? 0 : $d_neuron_survival_phenotype);
}

node SOD1_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_SOD1_rna : 0);
  rate_down = (@logic ? 0 : $d_SOD1_rna);
}

node SESN3_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_SESN3_rna : 0);
  rate_down = (@logic ? 0 : $d_SESN3_rna);
}

node PRKAA2_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_PRKAA2_rna : 0);
  rate_down = (@logic ? 0 : $d_PRKAA2_rna);
}

node ADCYAP1_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_ADCYAP1_rna : 0);
  rate_down = (@logic ? 0 : $d_ADCYAP1_rna);
}

node CFLAR_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_CFLAR_rna : 0);
  rate_down = (@logic ? 0 : $d_CFLAR_rna);
}

node VIP_rna {
  logic = (TF_NR4A2_complex);
  rate_up = (@logic ? $u_VIP_rna : 0);
  rate_down = (@logic ? 0 : $d_VIP_rna);
}

node pacemaking_activity_phenotype {
  logic = (KCNJ6_rna);
  rate_up = (@logic ? $u_pacemaking_activity_phenotype : 0);
  rate_down = (@logic ? 0 : $d_pacemaking_activity_phenotype);
}

node retinoic_acid_synthesis_phenotype {
  logic = (ALDH1A1_rna);
  rate_up = (@logic ? $u_retinoic_acid_synthesis_phenotype : 0);
  rate_down = (@logic ? 0 : $d_retinoic_acid_synthesis_phenotype);
}

node RGS6_rna {
  logic = (TF_PITX3_complex);
  rate_up = (@logic ? $u_RGS6_rna : 0);
  rate_down = (@logic ? 0 : $d_RGS6_rna);
}

node EN1 {
  logic = (NOT TF_PITX3_complex);
  rate_up = (@logic ? $u_EN1 : 0);
  rate_down = (@logic ? 0 : $d_EN1);
}
---------------------------------------------------------------------------------------------------------

----------------------------------------------- Variables -----------------------------------------------
$d_ADCYAP1_rna = 1;
$d_ALDH1A1_rna = 1;
$d_BDNF_rna = 1;
$d_CFLAR_rna = 1;
$d_COX5A_rna = 1;
$d_COX5B_rna = 1;
$d_COX6A1_rna = 1;
$d_COX8A_rna = 1;
$d_DCTN1_rna = 1;
$d_DDC_rna = 1;
$d_DRD2_rna = 1;
$d_DYNC1H1_rna = 1;
$d_EN1 = 1;
$d_EN1_rna = 1;
$d_FOXA2 = 1;
$d_FOXO1_rna = 1;
$d_FOXO3_rna = 1;
$d_GCH1_rna = 1;
$d_GDNF_rna = 1;
$d_KCNJ6_rna = 1;
$d_KIF1A_rna = 1;
$d_KLC1_rna = 1;
$d_LMX1A_rna = 1;
$d_LMX1B_rna = 1;
$d_LRRK2 = 1;
$d_MAP1B_rna = 1;
$d_MIR133B_rna = 1;
$d_NCOR2 = 1;
$d_NDUFB8_rna = 1;
$d_NKX6_1_rna = 1;
$d_NR4A2_nucleus = 1;
$d_NR4A2_rna = 1;
$d_NRF1_rna = 1;
$d_PARK7 = 1;
$d_PBX1 = 1;
$d_PIAS4 = 1;
$d_PIN1 = 1;
$d_PITX3 = 1;
$d_PITX3_rna = 1;
$d_PRKAA2_rna = 1;
$d_RET_rna = 1;
$d_RGS6_rna = 1;
$d_RXRA = 1;
$d_SESN3_rna = 1;
$d_SFPQ = 1;
$d_SLC18A2_rna = 1;
$d_SLC6A3_rna = 1;
$d_SNCA = 1;
$d_SOD1_rna = 1;
$d_TFEB_rna = 1;
$d_TF_FOXA1_2_complex = 1;
$d_TF_LMX1A_B_complex = 1;
$d_TF_NR4A2_complex = 1;
$d_TF_PITX3_complex = 1;
$d_TH_rna = 1;
$d_VIP_rna = 1;
$d_autophagy_phenotype = 1;
$d_axonal_transport_phenotype = 1;
$d_dopamine_metabolism_phenotype = 1;
$d_mitochondrial_biogenesis_phenotype = 1;
$d_neuron_survival_phenotype = 1;
$d_pacemaking_activity_phenotype = 1;
$d_retinoic_acid = 1;
$d_retinoic_acid_synthesis_phenotype = 1;
$nb_mutable = 0;
$u_ADCYAP1_rna = 1;
$u_ALDH1A1_rna = 1;
$u_BDNF_rna = 1;
$u_CFLAR_rna = 1;
$u_COX5A_rna = 1;
$u_COX5B_rna = 1;
$u_COX6A1_rna = 1;
$u_COX8A_rna = 1;
$u_DCTN1_rna = 1;
$u_DDC_rna = 1;
$u_DRD2_rna = 1;
$u_DYNC1H1_rna = 1;
$u_EN1 = 1;
$u_EN1_rna = 1;
$u_FOXA2 = 1;
$u_FOXO1_rna = 1;
$u_FOXO3_rna = 1;
$u_GCH1_rna = 1;
$u_GDNF_rna = 1;
$u_KCNJ6_rna = 1;
$u_KIF1A_rna = 1;
$u_KLC1_rna = 1;
$u_LMX1A_rna = 1;
$u_LMX1B_rna = 1;
$u_LRRK2 = 1;
$u_MAP1B_rna = 1;
$u_MIR133B_rna = 1;
$u_NCOR2 = 1;
$u_NDUFB8_rna = 1;
$u_NKX6_1_rna = 1;
$u_NR4A2_nucleus = 1;
$u_NR4A2_rna = 1;
$u_NRF1_rna = 1;
$u_PARK7 = 1;
$u_PBX1 = 1;
$u_PIAS4 = 1;
$u_PIN1 = 1;
$u_PITX3 = 1;
$u_PITX3_rna = 1;
$u_PRKAA2_rna = 1;
$u_RET_rna = 1;
$u_RGS6_rna = 1;
$u_RXRA = 1;
$u_SESN3_rna = 1;
$u_SFPQ = 1;
$u_SLC18A2_rna = 1;
$u_SLC6A3_rna = 1;
$u_SNCA = 1;
$u_SOD1_rna = 1;
$u_TFEB_rna = 1;
$u_TF_FOXA1_2_complex = 1;
$u_TF_LMX1A_B_complex = 1;
$u_TF_NR4A2_complex = 1;
$u_TF_PITX3_complex = 1;
$u_TH_rna = 1;
$u_VIP_rna = 1;
$u_autophagy_phenotype = 1;
$u_axonal_transport_phenotype = 1;
$u_dopamine_metabolism_phenotype = 1;
$u_mitochondrial_biogenesis_phenotype = 1;
$u_neuron_survival_phenotype = 1;
$u_pacemaking_activity_phenotype = 1;
$u_retinoic_acid = 1;
$u_retinoic_acid_synthesis_phenotype = 1;
---------------------------------------------------------------------------------------------------------

