begin name
friedland1
end name

begin reactions
r0 {1.0}ara = {1.0}$EXTERNAL
r10a {1.0}$EXTERNAL = {1.0}mT3cr
r10b {1.0}mT3cr = {1.0}$EXTERNAL
r11 {1.0}$EXTERNAL = {1.0}pT3
r12 {1.0}pT3 = {1.0}$EXTERNAL
r1a {1.0}$EXTERNAL = {1.0}taRNA
r1b {1.0}taRNA = {1.0}$EXTERNAL
r2a {1.0}$EXTERNAL = {1.0}mT7cr
r2b {1.0}mT7cr = {1.0}$EXTERNAL
r3a {1.0}$EXTERNAL = {1.0}mGFPcr
r3b {1.0}mGFPcr = {1.0}$EXTERNAL
r6 {1.0}$EXTERNAL = {1.0}pT7
r7 {1.0}$EXTERNAL = {1.0}pGFP
r8 {1.0}pT7 = {1.0}$EXTERNAL
r9 {1.0}pGFP = {1.0}$EXTERNAL
end reactions

begin rate equations
r0 = cell*Piecewise[{{cAra, pulseflag == 1 && ara[t] > 0}}, dAra*ara[t]]
r10a = cell*(s0mT3cr + (kpT7*pT7[t]^n7)/(km7^n7 + pT7[t]^n7))
r10b = cell*dmT3*mT3cr[t]
r11 = cell*(s0pT3*mT3cr[t] + spT3k*mT3cr[t]*taRNA[t])
r12 = cell*dpT3*pT3[t]
r1a = cell*(s0taRNA + (sT*ara[t])/(kara + ara[t]))
r1b = cell*dtaRNA*taRNA[t]
r2a = cell*s0mT7cr
r2b = cell*dmT7*mT7cr[t]
r3a = cell*(s0mGFPcr + (kpT3*pT3[t]^n3)/(km3^n3 + pT3[t]^n3))
r3b = cell*dmGFP*mGFPcr[t]
r6 = cell*(s0pT7*mT7cr[t] + spT7k*mT7cr[t]*taRNA[t])
r7 = cell*(s0pGFP*mGFPcr[t] + spGFPk*mGFPcr[t]*taRNA[t])
r8 = cell*dpT7*pT7[t]
r9 = cell*dpGFP*pGFP[t]
end rate equations

begin parameters
cAra = 0.0003
dAra = 0.1201
dmGFP = 0.07
dmT3 = 0.0701
dmT7 = 0.0706
dpGFP = 0.003
dpT3 = 0.0069
dpT7 = 0.0056
dtaRNA = 0.1177
kara = 0.0571
kpT3 = 3.006
kpT7 = 3.8009
km3 = 7.9075
km7 = 3.0455
n3 = 0.8892
n7 = 2.602
pulse1length = 11.0
pulse1start = 0.01
pulse2length = 11.0
pulse3length = 22.0
pulseconc = 0.01
pulseflag = 0.0
pulseinterval = 20.0
s0mGFPcr = 0.0123
s0mT3cr = 0.0003
s0mT7cr = 0.0252
s0pGFP = 0.1007
s0pT3 = 0.0
s0pT7 = 0.0003
s0taRNA = 0.0008
sT = 0.8467
spGFPk = 0.9923
spT3k = 0.0115
spT7k = 0.0766
cell = 1.0
end parameters

begin initial conditions
ara[0] = arai
mGFPcr[0] = mGFPcri
mT3cr[0] = mT3cri
mT7cr[0] = mT7cri
pGFP[0] = pGFPi
pT3[0] = pT3i
pT7[0] = pT7i
taRNA[0] = taRNAi
end initial conditions

begin initial values
arai = 0.0
mGFPcri = 0.176991329
mT3cri = 0.00566438
mT7cri = 0.3569405099
pGFPi = 6.338921181
pT3i = 6.41674e-05
pT7i = 0.05230744612
taRNAi = 0.006796941377
end initial values

begin assignment rules
pulse3start := pulse2length + pulse2start + pulseinterval
pulse2start := pulse1length + pulse1start + pulseinterval
end assignment rules

begin function definitions
end function definitions

begin events
pulse_start3 = (t >= pulse3start && t <= pulse3length + pulse3start, {ara[t] -> pulseconc, pulseflag -> 1}, 0)
pulse_end3 = (t > pulse3length + pulse3start, {pulseflag -> 0}, 0)
pulse_start2 = (t >= pulse2start && t <= pulse2length + pulse2start, {ara[t] -> pulseconc, pulseflag -> 1}, 0)
pulse_end2 = (t < pulse3start && t > pulse2length + pulse2start, {pulseflag -> 0}, 0)
pulse_end1 = (t < pulse2start && t > pulse1length + pulse1start, {pulseflag -> 0}, 0)
pulse_start1 = (t >= pulse1start && t <= pulse1length + pulse1start, {ara[t] -> pulseconc, pulseflag -> 1}, 0)
end events

begin process annotations
end process annotations

begin species annotations
ara http://identifiers.org/kegg.compound/C00259
ara http://identifiers.org/chebi/CHEBI:17535
end species annotations

begin units
end units