XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
#Readme: The author recommend to run the code in silent mode. The data will be output in test.txt. #When to do parameter sensitivity analysis, use command 'RANGE=1, RANGEOVER=step, RANGESTEP=1100, RANGELOW=0, RANGEHIGH=1100, RANGERESET=yes, RANGEOLDIC=yes, output=test1'. The data will be output in 1100 data file named test1.1 (step value), test1.2........ #A is BDNF activity, B is BDNF mRNA, CEBP is CEBP dA/dt=(stim + k_1*B^2/(B^2+k_trs^2)*(1-PSI*turn)-kdega*A/(A+K_A2)) dB/dt=((K_min_B +k_2*feed3) - kdegb*B/(B+K_B2)) feed3=(CEBP^2)/(K_BCEBP^2+CEBP^2)*(heav(t2+3600*endh-t))+kbcedbnf*(heav(t-t2-3600*endh)) endh=18 BDNF=A CREB1=CREBt-pCREB1 CREBt=0.085 pCREB1'=((K_phosC1+feed4)*CREB1-K_dephC1*pCREB1) feed4=k_Cbdnf*BDNF^2/(BDNF^2+K_bpcreb^2)*(1-PSI*0) #synthesis OF CEBP protein CEBP'=((feed2*v_cebp+K_min_C)*(CEBPmax-CEBP)*(1-PSI*turn)-K_dxCBP*CEBP/(CEBP+K_dCEBP)) feed2 =(pCREB1^2)/(k_crece^2+pCREB1^2)*heav(t-t2-3600*starth)+kbpcrebce*heav(t2+3600*starth-t) starth=6 CEBPmax=0.228 #W1 is pathway 1, W2 is pathway 2, W3 is synaptic weight W1'=((kbasw1+kfw1*(pCREB1-0.0066)/kw1creb*(CEBP-0.076)/kw1cebp*w1^2/(w1^2+kw1^2))*(1-PSI*turn)-kdw1*w1) w2'=((kbasw2+kfw2*(CEBP-0.076)/kw2cebp*w2^2/(w2^2+kw2^2))*(1-PSI*turn)-kdw2*w2) w3'=(kfw3*(W1+w2)*(1-PSI*turn)-kdw3*w3) # stimulus stim = test1*HEAV(T-t2)*HEAV(dur+t2-T)+0*(1-HEAV(T-t2)*HEAV(dur+t2-T)) t2=10000 # inhibitors PSI=amp*heav(t-t1)*heav(t1+duration-t) p amp=0 p turn=0 #ADD ODN #p amp=0.95 #ADD anti-BDNF #p amp=0.8 #ADD PSI #p amp=0.8 #duration for anti-BDNF #duration=3600*6 #duration for ODN #duration=3600*24 #duration for PSI duration=3600*6 # time to start inhbit t1=t2+3600*startIn startIn=24 init A=0.0722924 init B=0.00320135 init pCREB1=0.0066 init CEBP=0.076 init w1=100 init w2=100 init w3=100 #parameter sensitivity analysis K_BCEBP=1*(1+0.03*a4*heav(step+1)*heav(31-step)*HEAV(T-t2+7200)) k_trs=1*(1+0.03*a4*heav(step-30)*heav(62-step)*HEAV(T-t2+7200)) kdega=0.002*(1+0.03*a4*heav(step-61)*heav(93-step)*HEAV(T-t2+7200)) kdegb=0.0000226*(1+0.03*a4*heav(step-92)*heav(124-step)*HEAV(T-t2+7200)) K_bpcreb=5*(1+0.03*a4*heav(step-123)*heav(155-step)*HEAV(T-t2+7200)) K_B2=0.6*(1-0.03*a4*heav(step-154)*heav(186-step)*HEAV(T-t2+7200)) k_crece=2.24*(1+0.03*a4*heav(step-185)*heav(217-step)*HEAV(T-t2+7200)) K_min_B=0.000000078*(1-0.03*a4*heav(step-216)*heav(248-step)*HEAV(T-t2+7200)) k_1=21*(1-0.03*a4*heav(step-247)*heav(279-step)*HEAV(T-t2+7200)) K_dephC1=0.000024*(1+0.03*a4*heav(step-278)*heav(310-step)*HEAV(T-t2+7200)) K_dxCBP=0.00000565*(1+0.03*a4*heav(step-309)*heav(341-step)*HEAV(T-t2+7200)) kbcedbnf=0.00574*(1-0.03*a4*heav(step-340)*heav(372-step)*HEAV(T-t2+7200)) K_phosC1=0.0000008*(1-0.03*a4*heav(step-371)*heav(403-step)*HEAV(T-t2+7200)) k_2=0.00000726*(1-0.03*a4*heav(step-402)*heav(434-step)*HEAV(T-t2+7200)) k_Cbdnf=0.00592*(1-0.03*a4*heav(step-433)*heav(465-step)*HEAV(T-t2+7200)) K_A2=0.6*(1-0.03*a4*heav(step-464)*heav(496-step)*HEAV(T-t2+7200)) v_cebp=0.31*(1-0.03*a4*heav(step-495)*heav(527-step)*HEAV(T-t2+7200)) K_min_C=0.0000158*(1-0.03*a4*heav(step-526)*heav(558-step)*HEAV(T-t2+7200)) K_dCEBP=0.076*(1-0.03*a4*heav(step-557)*heav(589-step)*HEAV(T-t2+7200)) test1=0.03*(1-0.03*a4*heav(step-588)*heav(620-step)*HEAV(T-t2+7200)) dur=60*(1-0.03*a4*heav(step-619)*heav(651-step)*HEAV(T-t2+7200)) kbpcrebce=0.0000089*(1-0.03*a4*heav(step-650)*heav(682-step)*HEAV(T-t2+7200)) kbasw1=0.0004*(1-0.03*a4*heav(step-681)*heav(713-step)*HEAV(T-t2+7200)) kw1creb=0.198*(1+0.03*a4*heav(step-712)*heav(744-step)*HEAV(T-t2+7200)) kw1cebp=0.228*(1+0.03*a4*heav(step-743)*heav(775-step)*HEAV(T-t2+7200)) kfw1=1.2*(1-0.03*a4*heav(step-774)*heav(806-step)*HEAV(T-t2+7200)) kw1=150*(1+0.03*a4*heav(step-805)*heav(837-step)*HEAV(T-t2+7200)) kdw1=1/250000*(1+0.03*a4*heav(step-836)*heav(868-step)*HEAV(T-t2+7200)) kbasw2=1/100000*(1-0.03*a4*heav(step-867)*heav(899-step)*HEAV(T-t2+7200)) kw2cebp=0.228*(1+0.03*a4*heav(step-898)*heav(930-step)*HEAV(T-t2+7200)) kfw2=0.032*(1-0.03*a4*heav(step-929)*heav(961-step)*HEAV(T-t2+7200)) kw2=150*(1+0.03*a4*heav(step-960)*heav(992-step)*HEAV(T-t2+7200)) kdw2=1/10000000*(1+0.03*a4*heav(step-991)*heav(1023-step)*HEAV(T-t2+7200)) kdw3=0.00002*(1+0.03*a4*heav(step-1022)*heav(1054-step)*HEAV(T-t2+7200)) kfw3=0.00001*(1-0.03*a4*heav(step-1053)*heav(1085-step)*HEAV(T-t2+7200)) a4=(step-31*flr(step/31)) aux 0=(T-10000)/(3600*24) aux 1=stim aux 3=BDNF/0.072*100 aux 4=B/0.0032*100 aux 5=pCREB1/0.0066*100 aux 6=CEBP/0.076*100 aux 7=a4 p step=0 @ total=260000, xlo=0, xhi=5000, ylo=0, yhi=10, bounds=10e30, MAXSTOR=1300000,xp=vs, yp=mk,nout=2500, dt=0.05, @ output=test.txt #@ RANGE=1, RANGEOVER=step, RANGESTEP=1100, RANGELOW=0, RANGEHIGH=1100, RANGERESET=yes, RANGEOLDIC=yes, output=test1 d
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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:
- Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
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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 [69] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | amp
|
amp = 0 | F | 0.0 | None | |||
Parameter | turn
|
turn = 0 | F | 0.0 | None | |||
Parameter | a
|
a = 0.0722924 | F | 0.0722924 | None | |||
Parameter | b
|
b = 0.00320135 | F | 0.00320135 | None | |||
Parameter | pcreb1
|
pcreb1 = 0.0066 | F | 0.0066 | None | |||
Parameter | cebp
|
cebp = 0.076 | F | 0.076 | None | |||
Parameter | w1
|
w1 = 100 | F | 100.0 | None | |||
Parameter | w2
|
w2 = 100 | F | 100.0 | None | |||
Parameter | w3
|
w3 = 100 | F | 100.0 | None | |||
Parameter | step
|
step = 0 | F | 0.0 | None | |||
Parameter | feed3
|
F | 0.0 | dimensionless | None | |||
Parameter | endh
|
F | 0.0 | dimensionless | None | |||
Parameter | bdnf
|
F | 0.0 | dimensionless | None | |||
Parameter | creb1
|
F | 0.0 | dimensionless | None | |||
Parameter | crebt
|
F | 0.0 | dimensionless | None | |||
Parameter | feed4
|
F | 0.0 | dimensionless | None | |||
Parameter | feed2
|
F | 0.0 | dimensionless | None | |||
Parameter | starth
|
F | 0.0 | dimensionless | None | |||
Parameter | cebpmax
|
F | 0.0 | dimensionless | None | |||
Parameter | stim
|
F | 0.0 | dimensionless | None | |||
Parameter | t2
|
F | 0.0 | dimensionless | None | |||
Parameter | psi
|
F | 0.0 | dimensionless | None | |||
Parameter | duration
|
F | 0.0 | dimensionless | None | |||
Parameter | t1
|
F | 0.0 | dimensionless | None | |||
Parameter | startin
|
F | 0.0 | dimensionless | None | |||
Parameter | k_bcebp
|
F | 0.0 | dimensionless | None | |||
Parameter | k_trs
|
F | 0.0 | dimensionless | None | |||
Parameter | kdega
|
F | 0.0 | dimensionless | None | |||
Parameter | kdegb
|
F | 0.0 | dimensionless | None | |||
Parameter | k_bpcreb
|
F | 0.0 | dimensionless | None | |||
Parameter | k_b2
|
F | 0.0 | dimensionless | None | |||
Parameter | k_crece
|
F | 0.0 | dimensionless | None | |||
Parameter | k_min_b
|
F | 0.0 | dimensionless | None | |||
Parameter | k_1
|
F | 0.0 | dimensionless | None | |||
Parameter | k_dephc1
|
F | 0.0 | dimensionless | None | |||
Parameter | k_dxcbp
|
F | 0.0 | dimensionless | None | |||
Parameter | kbcedbnf
|
F | 0.0 | dimensionless | None | |||
Parameter | k_phosc1
|
F | 0.0 | dimensionless | None | |||
Parameter | k_2
|
F | 0.0 | dimensionless | None | |||
Parameter | k_cbdnf
|
F | 0.0 | dimensionless | None | |||
Parameter | k_a2
|
F | 0.0 | dimensionless | None | |||
Parameter | v_cebp
|
F | 0.0 | dimensionless | None | |||
Parameter | k_min_c
|
F | 0.0 | dimensionless | None | |||
Parameter | k_dcebp
|
F | 0.0 | dimensionless | None | |||
Parameter | test1
|
F | 0.0 | dimensionless | None | |||
Parameter | dur
|
F | 0.0 | dimensionless | None | |||
Parameter | kbpcrebce
|
F | 0.0 | dimensionless | None | |||
Parameter | kbasw1
|
F | 0.0 | dimensionless | None | |||
Parameter | kw1creb
|
F | 0.0 | dimensionless | None | |||
Parameter | kw1cebp
|
F | 0.0 | dimensionless | None | |||
Parameter | kfw1
|
F | 0.0 | dimensionless | None | |||
Parameter | kw1
|
F | 0.0 | dimensionless | None | |||
Parameter | kdw1
|
F | 0.0 | dimensionless | None | |||
Parameter | kbasw2
|
F | 0.0 | dimensionless | None | |||
Parameter | kw2cebp
|
F | 0.0 | dimensionless | None | |||
Parameter | kfw2
|
F | 0.0 | dimensionless | None | |||
Parameter | kw2
|
F | 0.0 | dimensionless | None | |||
Parameter | kdw2
|
F | 0.0 | dimensionless | None | |||
Parameter | kdw3
|
F | 0.0 | dimensionless | None | |||
Parameter | kfw3
|
F | 0.0 | dimensionless | None | |||
Parameter | a4
|
F | 0.0 | dimensionless | None | |||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | F | 0.0 | dimensionless | None | ||||
Parameter | t
|
model time | F | 0.0 | dimensionless | None |
type | Rules [66] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | d a/dt
|
= | None | ||||
Rule | d b/dt
|
= | None | ||||
Rule | d pcreb1/dt
|
= | None | ||||
Rule | d cebp/dt
|
= | None | ||||
Rule | d w1/dt
|
= | None | ||||
Rule | d w2/dt
|
= | None | ||||
Rule | d w3/dt
|
= | None | ||||
Rule | feed3
|
= | None | ||||
Rule | endh
|
= | None | ||||
Rule | bdnf
|
= | None | ||||
Rule | creb1
|
= | None | ||||
Rule | crebt
|
= | None | ||||
Rule | feed4
|
= | None | ||||
Rule | feed2
|
= | None | ||||
Rule | starth
|
= | None | ||||
Rule | cebpmax
|
= | None | ||||
Rule | stim
|
= | None | ||||
Rule | t2
|
= | None | ||||
Rule | psi
|
= | None | ||||
Rule | duration
|
= | None | ||||
Rule | t1
|
= | None | ||||
Rule | startin
|
= | None | ||||
Rule | k_bcebp
|
= | None | ||||
Rule | k_trs
|
= | None | ||||
Rule | kdega
|
= | None | ||||
Rule | kdegb
|
= | None | ||||
Rule | k_bpcreb
|
= | None | ||||
Rule | k_b2
|
= | None | ||||
Rule | k_crece
|
= | None | ||||
Rule | k_min_b
|
= | None | ||||
Rule | k_1
|
= | None | ||||
Rule | k_dephc1
|
= | None | ||||
Rule | k_dxcbp
|
= | None | ||||
Rule | kbcedbnf
|
= | None | ||||
Rule | k_phosc1
|
= | None | ||||
Rule | k_2
|
= | None | ||||
Rule | k_cbdnf
|
= | None | ||||
Rule | k_a2
|
= | None | ||||
Rule | v_cebp
|
= | None | ||||
Rule | k_min_c
|
= | None | ||||
Rule | k_dcebp
|
= | None | ||||
Rule | test1
|
= | None | ||||
Rule | dur
|
= | None | ||||
Rule | kbpcrebce
|
= | None | ||||
Rule | kbasw1
|
= | None | ||||
Rule | kw1creb
|
= | None | ||||
Rule | kw1cebp
|
= | None | ||||
Rule | kfw1
|
= | None | ||||
Rule | kw1
|
= | None | ||||
Rule | kdw1
|
= | None | ||||
Rule | kbasw2
|
= | None | ||||
Rule | kw2cebp
|
= | None | ||||
Rule | kfw2
|
= | None | ||||
Rule | kw2
|
= | None | ||||
Rule | kdw2
|
= | None | ||||
Rule | kdw3
|
= | None | ||||
Rule | kfw3
|
= | None | ||||
Rule | a4
|
= | None | ||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | = | None | |||||
Rule | t
|
= | None |