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
This file has been produced by sbmlutils.

Terms of use

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:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Model :

id
name
time
substance
extent
volume
area
length
Access SBML model  L3V1

FunctionDefinitions [4] name math sbo cvterm
max minimum x y x x y y
min maximum x y x x y y
heav heavyside x 0 x 0 0.5 x 0 1 x 0 0
mod modulo x y x y x y x 0 y 0 x y x y

Parameters [69] name constant value unit derived unit sbo cvterm
amp amp = 0 0.0 None
turn turn = 0 0.0 None
a a = 0.0722924 0.0722924 None
b b = 0.00320135 0.00320135 None
pcreb1 pcreb1 = 0.0066 0.0066 None
cebp cebp = 0.076 0.076 None
w1 w1 = 100 100.0 None
w2 w2 = 100 100.0 None
w3 w3 = 100 100.0 None
step step = 0 0.0 None
feed3 0.0 dimensionless None
endh 0.0 dimensionless None
bdnf 0.0 dimensionless None
creb1 0.0 dimensionless None
crebt 0.0 dimensionless None
feed4 0.0 dimensionless None
feed2 0.0 dimensionless None
starth 0.0 dimensionless None
cebpmax 0.0 dimensionless None
stim 0.0 dimensionless None
t2 0.0 dimensionless None
psi 0.0 dimensionless None
duration 0.0 dimensionless None
t1 0.0 dimensionless None
startin 0.0 dimensionless None
k_bcebp 0.0 dimensionless None
k_trs 0.0 dimensionless None
kdega 0.0 dimensionless None
kdegb 0.0 dimensionless None
k_bpcreb 0.0 dimensionless None
k_b2 0.0 dimensionless None
k_crece 0.0 dimensionless None
k_min_b 0.0 dimensionless None
k_1 0.0 dimensionless None
k_dephc1 0.0 dimensionless None
k_dxcbp 0.0 dimensionless None
kbcedbnf 0.0 dimensionless None
k_phosc1 0.0 dimensionless None
k_2 0.0 dimensionless None
k_cbdnf 0.0 dimensionless None
k_a2 0.0 dimensionless None
v_cebp 0.0 dimensionless None
k_min_c 0.0 dimensionless None
k_dcebp 0.0 dimensionless None
test1 0.0 dimensionless None
dur 0.0 dimensionless None
kbpcrebce 0.0 dimensionless None
kbasw1 0.0 dimensionless None
kw1creb 0.0 dimensionless None
kw1cebp 0.0 dimensionless None
kfw1 0.0 dimensionless None
kw1 0.0 dimensionless None
kdw1 0.0 dimensionless None
kbasw2 0.0 dimensionless None
kw2cebp 0.0 dimensionless None
kfw2 0.0 dimensionless None
kw2 0.0 dimensionless None
kdw2 0.0 dimensionless None
kdw3 0.0 dimensionless None
kfw3 0.0 dimensionless None
a4 0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [66]   assignment name derived units sbo cvterm
d a/dt = stim k_1 b 2 b 2 k_trs 2 1 psi turn kdega a a k_a2 None
d b/dt = k_min_b k_2 feed3 kdegb b b k_b2 None
d pcreb1/dt = k_phosc1 feed4 creb1 k_dephc1 pcreb1 None
d cebp/dt = feed2 v_cebp k_min_c cebpmax cebp 1 psi turn k_dxcbp cebp cebp k_dcebp None
d w1/dt = kbasw1 kfw1 pcreb1 0.0066 kw1creb cebp 0.076 kw1cebp w1 2 w1 2 kw1 2 1 psi turn kdw1 w1 None
d w2/dt = kbasw2 kfw2 cebp 0.076 kw2cebp w2 2 w2 2 kw2 2 1 psi turn kdw2 w2 None
d w3/dt = kfw3 w1 w2 1 psi turn kdw3 w3 None
feed3 = cebp 2 k_bcebp 2 cebp 2 heav t2 3600 endh t kbcedbnf heav t t2 3600 endh None
endh = 18 None
bdnf = a None
creb1 = crebt pcreb1 None
crebt = 0.085 None
feed4 = k_cbdnf bdnf 2 bdnf 2 k_bpcreb 2 1 psi 0 None
feed2 = pcreb1 2 k_crece 2 pcreb1 2 heav t t2 3600 starth kbpcrebce heav t2 3600 starth t None
starth = 6 None
cebpmax = 0.228 None
stim = test1 heav t t2 heav dur t2 t 0 1 heav t t2 heav dur t2 t None
t2 = 10000 None
psi = amp heav t t1 heav t1 duration t None
duration = 3600 6 None
t1 = t2 3600 startin None
startin = 24 None
k_bcebp = 1 1 0.03 a4 heav step 1 heav 31 step heav t t2 7200 None
k_trs = 1 1 0.03 a4 heav step 30 heav 62 step heav t t2 7200 None
kdega = 0.002 1 0.03 a4 heav step 61 heav 93 step heav t t2 7200 None
kdegb = 2.26 -5 1 0.03 a4 heav step 92 heav 124 step heav t t2 7200 None
k_bpcreb = 5 1 0.03 a4 heav step 123 heav 155 step heav t t2 7200 None
k_b2 = 0.6 1 0.03 a4 heav step 154 heav 186 step heav t t2 7200 None
k_crece = 2.24 1 0.03 a4 heav step 185 heav 217 step heav t t2 7200 None
k_min_b = 7.8 -8 1 0.03 a4 heav step 216 heav 248 step heav t t2 7200 None
k_1 = 21 1 0.03 a4 heav step 247 heav 279 step heav t t2 7200 None
k_dephc1 = 2.4 -5 1 0.03 a4 heav step 278 heav 310 step heav t t2 7200 None
k_dxcbp = 5.65 -6 1 0.03 a4 heav step 309 heav 341 step heav t t2 7200 None
kbcedbnf = 0.00574 1 0.03 a4 heav step 340 heav 372 step heav t t2 7200 None
k_phosc1 = 8 -7 1 0.03 a4 heav step 371 heav 403 step heav t t2 7200 None
k_2 = 7.26 -6 1 0.03 a4 heav step 402 heav 434 step heav t t2 7200 None
k_cbdnf = 0.00592 1 0.03 a4 heav step 433 heav 465 step heav t t2 7200 None
k_a2 = 0.6 1 0.03 a4 heav step 464 heav 496 step heav t t2 7200 None
v_cebp = 0.31 1 0.03 a4 heav step 495 heav 527 step heav t t2 7200 None
k_min_c = 1.58 -5 1 0.03 a4 heav step 526 heav 558 step heav t t2 7200 None
k_dcebp = 0.076 1 0.03 a4 heav step 557 heav 589 step heav t t2 7200 None
test1 = 0.03 1 0.03 a4 heav step 588 heav 620 step heav t t2 7200 None
dur = 60 1 0.03 a4 heav step 619 heav 651 step heav t t2 7200 None
kbpcrebce = 8.9 -6 1 0.03 a4 heav step 650 heav 682 step heav t t2 7200 None
kbasw1 = 0.0004 1 0.03 a4 heav step 681 heav 713 step heav t t2 7200 None
kw1creb = 0.198 1 0.03 a4 heav step 712 heav 744 step heav t t2 7200 None
kw1cebp = 0.228 1 0.03 a4 heav step 743 heav 775 step heav t t2 7200 None
kfw1 = 1.2 1 0.03 a4 heav step 774 heav 806 step heav t t2 7200 None
kw1 = 150 1 0.03 a4 heav step 805 heav 837 step heav t t2 7200 None
kdw1 = 1 250000 1 0.03 a4 heav step 836 heav 868 step heav t t2 7200 None
kbasw2 = 1 100000 1 0.03 a4 heav step 867 heav 899 step heav t t2 7200 None
kw2cebp = 0.228 1 0.03 a4 heav step 898 heav 930 step heav t t2 7200 None
kfw2 = 0.032 1 0.03 a4 heav step 929 heav 961 step heav t t2 7200 None
kw2 = 150 1 0.03 a4 heav step 960 heav 992 step heav t t2 7200 None
kdw2 = 1 10000000 1 0.03 a4 heav step 991 heav 1023 step heav t t2 7200 None
kdw3 = 2 -5 1 0.03 a4 heav step 1022 heav 1054 step heav t t2 7200 None
kfw3 = 1 -5 1 0.03 a4 heav step 1053 heav 1085 step heav t t2 7200 None
a4 = step 31 flr step 31 None
= t 10000 3600 24 None
= stim None
= bdnf 0.072 100 None
= b 0.0032 100 None
= pcreb1 0.0066 100 None
= cebp 0.076 100 None
= a4 None
t = time None