XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# This ODE code is a comparable implementation of the BGCT model described in the # following paper: # # Title: Bidirectional Control of Absence Seizures by the Basal Ganglia: A # Computational Evidence (2014) # Authors: Mingming Chen, Daqing Guo*, Tiebin Wang, Wei Jing, Yang Xia, Peng Xu, # Cheng Luo, Pedro A. Valdes-Sosa1, and Dezhong Yao* # Journal: PLoS Computational Biology # Emails: twqylsf@gmail.com and dqguo@uestc.edu.cn # You can use XPPAut (http://www.math.pitt.edu/~bard/xpp/xpp.html) for runing this code. # # Intergation step dt=0.00005 # Simulation time time=13 # SNr-TRN pathway, 1 open and 0 close p open1=1 # SNr-SRN pathway, 1 open and 0 close p open2=1 # Scale factor p KK=1 # Maximum firing rate (Table 1 A) Qmax_i=250 Qmax_d1=65 Qmax_d2=65 Qmax_p1=250 Qmax_p2=300 Qmax_xi=500 Qmax_s=250 Qmax_r=250 # Mean firing threshold (Table 1 B) theta_i=15e-3 theta_d1=19e-3 theta_d2=19e-3 theta_p1=10e-3 theta_p2=9e-3 theta_xi=1e-2 theta_s=15e-3 theta_r=15e-3 # Coupling strength (Table 1 C) v_ee=1.0e-3 v_ei=1.8e-3 v_re=5.0e-5 v_rs=5.0e-4 v_d1e=1.0e-3 v_d1d1=2.0e-4 v_d1s=1.0e-4 v_d2e=7.0e-4 v_d2d2=3.0e-4 v_d2s=5e-5 v_p1d1=1.0e-4 v_p1p2=3.0e-5 v_p2d2=3.0e-4 v_p2p2=0.75e-4 v_p2xi=4.5e-4 v_xip2=4.0e-5 v_es=1.8e-3 v_se=2.2e-3 v_xie=0.1e-3 # Other parameters (Table 1 D) gamma_e=100 alpha=50 beta=200 sigma=0.006 v_sn_phi_n=2.0e-3 # TRN-SRN p v_sr=8.0e-4 # STN-SNr p v_p1xi=3e-4 # delay parameter p tau=0.05 v_sp1=open2*3.5e-5 v_rp1=KK*open1*3.5e-5 # random initial condition init x[1]=0.5*0*ran; x[2]=-1500+6000*ran; x[3]=0.02*ran; x[4]=-2*3.5*ran; x[5]=0.04*ran init x[6]=-0.7+1.5*ran; x[7]=0.001+0.025*ran; x[8]=-0.4+ran; x[9]=0.004+0.013*ran init x[10]=-0.15+0.4*ran; x[11]=0.0005+0.0035*ran; x[12]=-0.12+0.22*ran; x[13]=-0.001+0.0055*ran init x[14]=-0.1+0.2*ran; x[15]=-0.09+0.1*ran; x[16]=-4+7*ran; x[17]=0.025*ran; x[18]=-0.6+2*ran # sigmoid function for different neural populations S_i=Qmax_i/(1+exp(-pi/sqrt(3)*(x3-theta_i)/sigma)) S_d1=Qmax_d1/(1+exp(-pi/sqrt(3)*(x5-theta_d1)/sigma)) S_d2=Qmax_d2/(1+exp(-pi/sqrt(3)*(x7-theta_d2)/sigma)) S_p1=Qmax_p1/(1+exp(-pi/sqrt(3)*(x9-theta_p1)/sigma)) S_p2=Qmax_p2/(1+exp(-pi/sqrt(3)*(x11-theta_p2)/sigma)) S_xi=Qmax_xi/(1+exp(-pi/sqrt(3)*(x13-theta_xi)/sigma)) S_s=Qmax_s/(1+exp(-pi/sqrt(3)*(x15-theta_s)/sigma)) S_r=Qmax_r/(1+exp(-pi/sqrt(3)*(x17-theta_r)/sigma)) S_r_lag=Qmax_r/(1+exp(-pi/sqrt(3)*(delay(x17,tau)-theta_r)/sigma)) # --------------------------------cerebral cortex---------------------------------------- x1'=x2 x2'=gamma_e^2*(-x1+S_i)-2*gamma_e*x2 x3'=x4 x4'=alpha*beta*(-x3+v_ee*x1+v_es*S_s-v_ei*S_i)-(alpha+beta)*x4 # ---------------------------------striatum D1-------------------------------------------- x5'=x6 x6'=alpha*beta*(-x5+v_d1e*x1-v_d1d1*S_d1+v_d1s*S_s)-(alpha+beta)*x6 # ---------------------------------striatum D2-------------------------------------------- x7'=x8 x8'=alpha*beta*(-x7+v_d2e*x1-v_d2d2*S_d2+v_d2s*S_s)-(alpha+beta)*x8 # ----------------------------------SNr/GPi----------------------------------------------- x9'=x10 x10'=alpha*beta*(-x9-v_p1d1*S_d1-v_p1p2*S_p2+v_p1xi*S_xi)-(alpha+beta)*x10 # -----------------------------------GPe-------------------------------------------------- x11'=x12 x12'=alpha*beta*(-x11-v_p2d2*S_d2-v_p2p2*S_p2+v_p2xi*S_xi)-(alpha+beta)*x12 # ------------------------------------STN------------------------------------------------- x13'=x14 x14'=alpha*beta*(-x13+v_xie*x1-v_xip2*S_p2)-(alpha+beta)*x14 # ------------------------------------SRN-------------------------------------------------- x15'=x16 x16'=alpha*beta*(-x15-v_sp1*S_p1+v_se*x1-v_sr*S_r-v_sr*S_r_lag+v_sn_phi_n)-(alpha+beta)*x16 # -----------------------------------TRN-------------------------------------------------- x17'=x18 x18'=alpha*beta*(-x17-v_rp1*S_p1+v_rs*S_s+v_re*x1)-(alpha+beta)*x18 @ xlo=0, ylo=-10, xhi=13, yhi=150, yp=x1 @ total=13, dt=0.00005, bounds=10e10, maxstore=10e15, delay=1 done
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Copyright © 2017 Matthias Koenig
Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:
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Model :
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type | FunctionDefinitions [4] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max
|
minimum | |||
FunctionDefinition | min
|
maximum | |||
FunctionDefinition | heav
|
heavyside | |||
FunctionDefinition | mod
|
modulo |
type | Parameters [114] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | open1
|
open1 = 1 | F | 1.0 | None | |||
Parameter | open2
|
open2 = 1 | F | 1.0 | None | |||
Parameter | kk
|
kk = 1 | F | 1.0 | None | |||
Parameter | v_sr
|
v_sr = 8.0e-4 | F | 0.0008 | None | |||
Parameter | v_p1xi
|
v_p1xi = 3e-4 | F | 0.0003 | None | |||
Parameter | tau
|
tau = 0.05 | F | 0.05 | None | |||
Parameter | x[1] | F | 0.0 | None | ||||
Parameter | x[2] | F | 0.0 | None | ||||
Parameter | x[3] | F | 0.0 | None | ||||
Parameter | x[4] | F | 0.0 | None | ||||
Parameter | x[5] | F | 0.0 | None | ||||
Parameter | x[6] | F | 0.0 | None | ||||
Parameter | x[7] | F | 0.0 | None | ||||
Parameter | x[8] | F | 0.0 | None | ||||
Parameter | x[9] | F | 0.0 | None | ||||
Parameter | x[10] | F | 0.0 | None | ||||
Parameter | x[11] | F | 0.0 | None | ||||
Parameter | x[12] | F | 0.0 | None | ||||
Parameter | x[13] | F | 0.0 | None | ||||
Parameter | x[14] | F | 0.0 | None | ||||
Parameter | x[15] | F | 0.0 | None | ||||
Parameter | x[16] | F | 0.0 | None | ||||
Parameter | x[17] | F | 0.0 | None | ||||
Parameter | x[18] | F | 0.0 | None | ||||
Parameter | x[1] = 0.5*0*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[2] = -1500+6000*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[3] = 0.02*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[4] = -2*3.5*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[5] = 0.04*ran | T | 0.0 | dimensionless | None | |||
Parameter | x[6] = -0.7+1.5*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[7] = 0.001+0.025*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[8] = -0.4+ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[9] = 0.004+0.013*ran | T | 0.0 | dimensionless | None | |||
Parameter | x[10] = -0.15+0.4*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[11] = 0.0005+0.0035*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[12] = -0.12+0.22*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[13] = -0.001+0.0055*ran | T | 0.0 | dimensionless | None | |||
Parameter | x[14] = -0.1+0.2*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[15] = -0.09+0.1*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[16] = -4+7*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[17] = 0.025*ran; | T | 0.0 | dimensionless | None | |||
Parameter | x[18] = -0.6+2*ran | T | 0.0 | dimensionless | None | |||
Parameter | x1
|
F | 0.0 | dimensionless | None | |||
Parameter | x2
|
F | 0.0 | dimensionless | None | |||
Parameter | x3
|
F | 0.0 | dimensionless | None | |||
Parameter | x4
|
F | 0.0 | dimensionless | None | |||
Parameter | x5
|
F | 0.0 | dimensionless | None | |||
Parameter | x6
|
F | 0.0 | dimensionless | None | |||
Parameter | x7
|
F | 0.0 | dimensionless | None | |||
Parameter | x8
|
F | 0.0 | dimensionless | None | |||
Parameter | x9
|
F | 0.0 | dimensionless | None | |||
Parameter | x10
|
F | 0.0 | dimensionless | None | |||
Parameter | x11
|
F | 0.0 | dimensionless | None | |||
Parameter | x12
|
F | 0.0 | dimensionless | None | |||
Parameter | x13
|
F | 0.0 | dimensionless | None | |||
Parameter | x14
|
F | 0.0 | dimensionless | None | |||
Parameter | x15
|
F | 0.0 | dimensionless | None | |||
Parameter | x16
|
F | 0.0 | dimensionless | None | |||
Parameter | x17
|
F | 0.0 | dimensionless | None | |||
Parameter | x18
|
F | 0.0 | dimensionless | None | |||
Parameter | dt
|
F | 0.0 | dimensionless | None | |||
Parameter | time
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_i
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_d1
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_d2
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_p1
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_p2
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_xi
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_s
|
F | 0.0 | dimensionless | None | |||
Parameter | qmax_r
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_i
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_d1
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_d2
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_p1
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_p2
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_xi
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_s
|
F | 0.0 | dimensionless | None | |||
Parameter | theta_r
|
F | 0.0 | dimensionless | None | |||
Parameter | v_ee
|
F | 0.0 | dimensionless | None | |||
Parameter | v_ei
|
F | 0.0 | dimensionless | None | |||
Parameter | v_re
|
F | 0.0 | dimensionless | None | |||
Parameter | v_rs
|
F | 0.0 | dimensionless | None | |||
Parameter | v_d1e
|
F | 0.0 | dimensionless | None | |||
Parameter | v_d1d1
|
F | 0.0 | dimensionless | None | |||
Parameter | v_d1s
|
F | 0.0 | dimensionless | None | |||
Parameter | v_d2e
|
F | 0.0 | dimensionless | None | |||
Parameter | v_d2d2
|
F | 0.0 | dimensionless | None | |||
Parameter | v_d2s
|
F | 0.0 | dimensionless | None | |||
Parameter | v_p1d1
|
F | 0.0 | dimensionless | None | |||
Parameter | v_p1p2
|
F | 0.0 | dimensionless | None | |||
Parameter | v_p2d2
|
F | 0.0 | dimensionless | None | |||
Parameter | v_p2p2
|
F | 0.0 | dimensionless | None | |||
Parameter | v_p2xi
|
F | 0.0 | dimensionless | None | |||
Parameter | v_xip2
|
F | 0.0 | dimensionless | None | |||
Parameter | v_es
|
F | 0.0 | dimensionless | None | |||
Parameter | v_se
|
F | 0.0 | dimensionless | None | |||
Parameter | v_xie
|
F | 0.0 | dimensionless | None | |||
Parameter | gamma_e
|
F | 0.0 | dimensionless | None | |||
Parameter | alpha
|
F | 0.0 | dimensionless | None | |||
Parameter | beta
|
F | 0.0 | dimensionless | None | |||
Parameter | sigma
|
F | 0.0 | dimensionless | None | |||
Parameter | v_sn_phi_n
|
F | 0.0 | dimensionless | None | |||
Parameter | v_sp1
|
F | 0.0 | dimensionless | None | |||
Parameter | v_rp1
|
F | 0.0 | dimensionless | None | |||
Parameter | s_i
|
F | 0.0 | dimensionless | None | |||
Parameter | s_d1
|
F | 0.0 | dimensionless | None | |||
Parameter | s_d2
|
F | 0.0 | dimensionless | None | |||
Parameter | s_p1
|
F | 0.0 | dimensionless | None | |||
Parameter | s_p2
|
F | 0.0 | dimensionless | None | |||
Parameter | s_xi
|
F | 0.0 | dimensionless | None | |||
Parameter | s_s
|
F | 0.0 | dimensionless | None | |||
Parameter | s_r
|
F | 0.0 | dimensionless | None | |||
Parameter | s_r_lag
|
F | 0.0 | dimensionless | None | |||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | InitialAssignments [18] | name | assignment | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | ||||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | ||||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | ||||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = | None | |||||
InitialAssignment | = |
type | Rules [72] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d x1/dt
|
= | None | ||||
Rule | d x2/dt
|
= | None | ||||
Rule | d x3/dt
|
= | None | ||||
Rule | d x4/dt
|
= | None | ||||
Rule | d x5/dt
|
= | None | ||||
Rule | d x6/dt
|
= | None | ||||
Rule | d x7/dt
|
= | None | ||||
Rule | d x8/dt
|
= | None | ||||
Rule | d x9/dt
|
= | None | ||||
Rule | d x10/dt
|
= | None | ||||
Rule | d x11/dt
|
= | None | ||||
Rule | d x12/dt
|
= | None | ||||
Rule | d x13/dt
|
= | None | ||||
Rule | d x14/dt
|
= | None | ||||
Rule | d x15/dt
|
= | None | ||||
Rule | d x16/dt
|
= | None | ||||
Rule | d x17/dt
|
= | None | ||||
Rule | d x18/dt
|
= | None | ||||
Rule | dt
|
= | None | ||||
Rule | time
|
= | None | ||||
Rule | qmax_i
|
= | None | ||||
Rule | qmax_d1
|
= | None | ||||
Rule | qmax_d2
|
= | None | ||||
Rule | qmax_p1
|
= | None | ||||
Rule | qmax_p2
|
= | None | ||||
Rule | qmax_xi
|
= | None | ||||
Rule | qmax_s
|
= | None | ||||
Rule | qmax_r
|
= | None | ||||
Rule | theta_i
|
= | None | ||||
Rule | theta_d1
|
= | None | ||||
Rule | theta_d2
|
= | None | ||||
Rule | theta_p1
|
= | None | ||||
Rule | theta_p2
|
= | None | ||||
Rule | theta_xi
|
= | None | ||||
Rule | theta_s
|
= | None | ||||
Rule | theta_r
|
= | None | ||||
Rule | v_ee
|
= | None | ||||
Rule | v_ei
|
= | None | ||||
Rule | v_re
|
= | None | ||||
Rule | v_rs
|
= | None | ||||
Rule | v_d1e
|
= | None | ||||
Rule | v_d1d1
|
= | None | ||||
Rule | v_d1s
|
= | None | ||||
Rule | v_d2e
|
= | None | ||||
Rule | v_d2d2
|
= | None | ||||
Rule | v_d2s
|
= | None | ||||
Rule | v_p1d1
|
= | None | ||||
Rule | v_p1p2
|
= | None | ||||
Rule | v_p2d2
|
= | None | ||||
Rule | v_p2p2
|
= | None | ||||
Rule | v_p2xi
|
= | None | ||||
Rule | v_xip2
|
= | None | ||||
Rule | v_es
|
= | None | ||||
Rule | v_se
|
= | None | ||||
Rule | v_xie
|
= | None | ||||
Rule | gamma_e
|
= | None | ||||
Rule | alpha
|
= | None | ||||
Rule | beta
|
= | None | ||||
Rule | sigma
|
= | None | ||||
Rule | v_sn_phi_n
|
= | None | ||||
Rule | v_sp1
|
= | None | ||||
Rule | v_rp1
|
= | None | ||||
Rule | s_i
|
= | None | ||||
Rule | s_d1
|
= | None | ||||
Rule | s_d2
|
= | None | ||||
Rule | s_p1
|
= | None | ||||
Rule | s_p2
|
= | None | ||||
Rule | s_xi
|
= | None | ||||
Rule | s_s
|
= | None | ||||
Rule | s_r
|
= | None | ||||
Rule | s_r_lag
|
= | None | ||||
Rule | t
|
= | None |