pre-release beta2

SI/Gq_parameters.csv

 Parameter,Value,Unit
-Gq_a_GDP_init:0.0027739,uM
-Gq_a_GDP_init:6.4172E-4,uM
-Gq_bg_init:0.0037173,uM
-RGS4_init:0.019994,uM
-RGS4_Gq_a_GTP_init:6.4168E-6,uM
-Ca_init:0.1,uM
-PLCb_init:0.090022,uM
-PLCb_Gq_a_GTP_init:1.4492E-4,uM
-PLCb_Ca_init:0.0093825,uM
-PLCb_Ca_Gq_a_GTP_init:1.5038E-4,uM
-PIP2_init:2.6578,uM
-IP3_init:0.21952,uM
-DAG_init:0.055555,uM
-R_Gq_trimer_init:0,uM
-R_L_Gq_trimer_init:0,uM
-Gq_trimer_init:0.61869,uM
-RL_kon:1.00,uM-1*s-1
-RL_koff:0.0046,s-1
-Gqa_Gqbg_kon:6.0,uM-1*s-1
-Gqa_Gqbg_koff:0.0001,s-1
-RL_Gq_decay:0.04,s-1
-RGS4_Gq_a_GTP_kon:20.83,uM-1*s-1
-RGS4_Gq_a_GTP_koff:33.32,s-1
-RGS4_Gq_a_GTP_decay:8.33,s-1
-Gq_a_GTP_decay:0.01,s-1
-Gq_a_GTP_PLCb_kon:2.52,uM-1*s-1
-Gq_a_GTP_PLCb_off:1.00,s-1
-Gq_a_GTP_PLCb_Ca_kon:30.0,uM-1*s-1
-Gq_a_GTP_PLCb_Ca_koff:1.00,s-1
-Gq_a_GTP_PLCb_Ca_decay:0.013,s-1
-PLCb_Ca_kon:3.00,uM-1*s-1
-PLCb_Ca_koff:1.00,s-1
-PLCb_Ca_Gq_a_GTP_kon:25.2,uM-1*s-1
-PLCb_Ca_Gq_a_GTP_koff:1.00,s-1
-DAG_decay:0.15,s-1
-
+time_in,0,s
+time_out,0,s
+Gq_a_GDP_init,0.0027739,uM
+Gq_a_GDP_init,6.4172E-4,uM
+Gq_bg_init,0.0037173,uM
+RGS4_init,0.019994,uM
+RGS4_Gq_a_GTP_init,6.4168E-6,uM
+Ca_init,0.1,uM
+PLCb_init,0.090022,uM
+PLCb_Gq_a_GTP_init,1.4492E-4,uM
+PLCb_Ca_init,0.0093825,uM
+PLCb_Ca_Gq_a_GTP_init,1.5038E-4,uM
+PIP2_init,2.6578,uM
+IP3_init,0.21952,uM
+DAG_init,0.055555,uM
+R_Gq_trimer_init,0,uM
+R_L_Gq_trimer_init,0,uM
+Gq_trimer_init,0.61869,uM
+RL_kon,1.00,uM-1*s-1
+RL_koff,0.0046,s-1
+Gqa_Gqbg_kon,6.0,uM-1*s-1
+Gqa_Gqbg_koff,0.0001,s-1
+RL_Gq_decay,0.04,s-1
+RGS4_Gq_a_GTP_kon,20.83,uM-1*s-1
+RGS4_Gq_a_GTP_koff,33.32,s-1
+RGS4_Gq_a_GTP_decay,8.33,s-1
+Gq_a_GTP_decay,0.01,s-1
+Gq_a_GTP_PLCb_kon,2.52,uM-1*s-1
+Gq_a_GTP_PLCb_off,1.00,s-1
+Gq_a_GTP_PLCb_Ca_kon,30.0,uM-1*s-1
+Gq_a_GTP_PLCb_Ca_koff,1.00,s-1
+Gq_a_GTP_PLCb_Ca_decay,0.013,s-1
+PLCb_Ca_kon,3.00,uM-1*s-1
+PLCb_Ca_koff,1.00,s-1
+PLCb_Ca_Gq_a_GTP_kon,25.2,uM-1*s-1
+PLCb_Ca_Gq_a_GTP_koff,1.00,s-1
+DAG_decay,0.15,s-1
+PIP2_Gq_a_GTP_PLCb_Ca_k,(48.0 * [PIP2])/(5.00 + [PIP2])),DO NOT CHANGE
+PIP2_PLCb_Ca_k,(10.0 * [PIP2])/(40.13 + [PIP2])),DO NOT CHANGE
+IP3_deg_k,(0.14*([IP3] - [IP3_init]))/[IP3]),DO NOT CHANGE
 

SI/Gq_reactions.csv

-Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s)
+Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s)
 
+1,R + L <-> RL,RL_kon,RL_koff
+2,RL + Gq_a(GDP)*Gq_bg <-> R*Gq_a(GDP)*Gq_bg,R_L_Gq_trimer_kf,R_L_Gq_trimer_kr
+3,Gq_a(GDP) + Gq_bg <-> Gq_a(GDP)*Gq_bg,Gq_trimerization_k,Gq_trimer_split_k
+4,R*Gq_a(GDP)*Gq_bg -> R + Gq_a(GTP) + Gq_bg,,R_L_Gq_trimer_split_k
+5,RGS4 + Gq_a(GTP) <-> RGS4*Gq_a(GTP),RGS4_Gq_a_GTP_kf,RGS4_Gq_a_GTP_kr
+6,RGS4*Gq_a(GTP) -> RGS4 + Gq_a(GDP),,RGS4_Gq_a_GTP_diss_k
+7,Gq_a(GTP) -> Gq_a(GDP),,Gq_a_GTP_decay_k
+8,Gq_a(GTP) + PLCb <-> Gq_a(GTP)*PLCb,Gq_a_GTP_PLCb_kf,Gq_a_GTP_PLCb_kr
+9,Gq_a(GTP)*PLCb + Ca <-> Gq_a(GTP)*PLCb*Ca,Gq_a_GTP_PLCb_Ca_kf,Gq_a_GTP_PLCb_Ca_kr
+10,Gq_a(GTP)*PLCb*Ca -> Gq_a(GDP) + PLCb*Ca,,Gq_a_GTP_PLCb_Ca_decay_k
+11,PLCb + Ca <-> PLCb*Ca, PLCb_Ca_kf,PLCb_Ca_kr
+12,PLCb*Ca + Gq_a(GTP) <-> Gq_a(GTP)*PLCb*Ca,PLCb_Ca_Gq_a_GTP_kf,PLCb_Ca_Gq_a_GTP_kr
+13,PLCb*Ca -> IP3 + DAG + PLCb*Ca,,PIP2_PLCb_Ca_k
+14,Gq_a(GTP)*PLCb*Ca -> IP3 + DAG + Gq_a(GTP)*PLCb*Ca,,PIP2_Gq_a_GTP_PLCb_Ca_k
+15,IP3 -> None,,IP3_deg_k
+16,DAG -> None,,DAG_deg_k    
+    
\ No newline at end of file

SI/OXTR_pathway_parameters.csv

+Parameter,Value,Unit
+time_in,50,s
+time_out,51,s
+L_init,0.1,uM
+R_init,1.4107*0.73,uM
+PIP2_init,2.6578,uM
+Gq_a_GDP_init,0.0027739,uM
+Gq_a_GTP_init,6.4172E-4,uM
+Gq_bg_init,0.0037173,uM
+RGS4_init,0.019994,uM
+RGS4_Gq_a_GTP_init,6.4168E-6,uM
+Ca_init,0.1,uM
+CaER_init,1,uM
+PLCb_init,0.090022,uM
+PLCb_Gq_a_GTP_init,1.4492E-4,uM
+PLCb_Ca_init,0.0093825,uM
+PLCb_Ca_Gq_a_GTP_init,1.5038E-4,uM
+IP3_init,0.21952,uM
+DAG_init,0.055555,uM
+IP3R_init,0.119,uM
+R_Gq_trimer_init,1.4107*0.27,uM
+R_L_Gq_trimer_init,0,uM
+Gq_trimer_init,0.61869,uM
+R_L_kf,1.00,uM-1*s-1
+R_L_kr,2.50,s-1
+R_Gq_trimer_kf,1.00,uM-1*s-1
+R_Gq_trimer_kr,1.67,s-1
+R_L_Gq_trimer_kf,1.0,uM-1*s-1
+R_L_Gq_trimer_kr,0.0046,s-1
+Gq_trimerization_k,6.0,uM-1*s-1
+Gq_trimer_split_k,0.0001,s-1
+R_L_Gq_trimer_split_k,0.04,s-1
+RGS4_Gq_a_GTP_kf,20.83,uM-1*s-1
+RGS4_Gq_a_GTP_kr,33.32,s-1
+RGS4_Gq_a_GTP_diss_k,8.33,s-1
+Gq_a_GTP_decay_k,0.01,s-1
+Gq_a_GTP_PLCb_kf,2.52,uM-1*s-1
+Gq_a_GTP_PLCb_kr,1.00,s-1
+Gq_a_GTP_PLCb_Ca_kf,30.0,uM-1*s-1
+Gq_a_GTP_PLCb_Ca_kr,1.00,s-1
+Gq_a_GTP_PLCb_Ca_decay_k,0.013,s-1
+PLCb_Ca_kf,3.00,uM-1*s-1
+PLCb_Ca_kr,1.00,s-1
+PLCb_Ca_Gq_a_GTP_kf,25.2,uM-1*s-1
+PLCb_Ca_Gq_a_GTP_kr,1.00,s-1
+DAG_deg_k,0.15,s-1
+IP3R_IP3_kf,50,uM-1*s-1
+IPR3_IP3_kr,6.5,s-1
+IP3R_Ca_kf,20.0,uM-1*s-1
+IPR3_Ca_kr,0.0806,s-1
+IP3R_IP3_Ca_kf,1.0,uM-1*s-1
+IPR3_IP3_Ca_kr,0.5,s-1
+IP3R_Ca_IP3_kf,20.0,uM-1*s-1
+IPR3_Ca_IP3_kr,14.5,s-1
+v1,800,
+v8,0.15,
+v4,0.5,
+k4,0.09,
+c2,0.185,
+PIP2_PLCb_Ca_k,(10.0*[PIP2])/(40.13+[PIP2])),DONOTCHANGE
+PIP2_Gq_a_GTP_PLCb_Ca_k,(48.0*[PIP2])/(5.00+[PIP2])),DONOTCHANGE
+IP3_deg_k,(0.14*([IP3]-[IP3_init]))/[IP3]),DONOTCHANGE
+CaER_release_k,(c2*(v1*(([IP3R_IP3]/[IP3_init])**4)+v8)*([CaER]-[Ca]))),DONOTCHANGE
+Ca_inwards_k,(v4*([Ca]**2)/(([Ca]**2)+(k4**2)))/[Ca]),DONOTCHANGE
\ No newline at end of file

SI/OXTR_pathway_reactions.csv

+Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s)
+1,R + L <-> RL,R_L_kf,R_L_kr
+2,R + Gq <-> R*Gq,R_Gq_trimer_kf,R_Gq_trimer_kr
+3,RL + Gq <-> RLGq,R_L_Gq_trimer_kf,R_L_Gq_trimer_kr
+4,Gq_a + Gq_bg <-> Gq,Gq_trimerization_k,Gq_trimer_split_k
+5,RGq -> R + Gq_a + Gq_bg,,R_L_Gq_trimer_split_k
+6,RGS4 + Gq_a <-> RGS4*Gq_a,RGS4_Gq_a_GTP_kf,RGS4_Gq_a_GTP_kr
+7,RGS4*Gq_a -> RGS4 + Gq_a,,RGS4_Gq_a_GTP_diss_k
+8,Gq_a(GTP) -> Gq_a(GDP),,Gq_a_GTP_decay_k
+9,Gq_a + PLCb <-> Gq_a*PLCb,Gq_a_GTP_PLCb_kf,Gq_a_GTP_PLCb_kr
+10,Gq_a*PLCb + Ca <-> Gq_a*PLCb*Ca,Gq_a_GTP_PLCb_Ca_kf,Gq_a_GTP_PLCb_Ca_kr
+11,Gq_a(GTP)*PLCb*Ca -> Gq_a(GDP) + PLCb*Ca,,Gq_a_GTP_PLCb_Ca_decay_k
+12,PLCb + Ca <-> PLCb*Ca,PLCb_Ca_kf,PLCb_Ca_kr
+13,PLCb*Ca + Gq_a(GTP) <-> Gq_a(GTP)*PLCb*Ca,PLCb_Ca_Gq_a_GTP_kf,PLCb_Ca_Gq_a_GTP_kr
+14,PLCb*Ca -> IP3 + DAG + PLCb*Ca,,PIP2_PLCb_Ca_k 
+15,Gq_a(GTP)*PLCb*Ca -> IP3 + DAG + Gq_a(GTP)*PLCb*Ca,,PIP2_Gq_a_GTP_PLCb_Ca_k 
+16,IP3 -> None,,IP3_deg_k
+17,DAG -> None,,DAG_deg_k
+18,IP3R + IP3 <-> IP3R*IP3,IP3R_IP3_kf,IPR3_IP3_kr
+19,IP3R + Ca <-> IP3R*Ca,IP3R_Ca_kf,IPR3_Ca_kr
+20,IP3R*IP3 + Ca <-> IP3R*IP3*Ca,IP3R_IP3_Ca_kf,IPR3_IP3_Ca_kr
+21,IP3R*Ca + IP3 <-> IP3R*IP3*Ca,IP3R_Ca_IP3_kf,IPR3_Ca_IP3_kr
+22,None -> Ca,,CaER_release_k
+23,Ca -> None,,Ca_inwards_k