#file repressilator.ode
#Model of repressilator oscillatory genetic circuit
#from Elowitz and Leibler (2000) Nature 403, pp 335-338.
#Figure 7.21A
#ouput should be scaled by: 
# protein concentration *40, time/0.3485 as described in the caption

par alpha0=0.03
par alpha=298.2
par n=2
par beta=1/5

#model equations
m1' = alpha0 + alpha/(1+p3^n) - m1
p1' = beta*(m1-p1)
m2' = alpha0 + alpha/(1+p1^n) - m2
p2' = beta*(m2-p2)
m3' = alpha0 + alpha/(1+p2^n) - m3
p3' = beta*(m3-p3)

# initial condition
init m1=0.2, p1=0.1, m2=0.3, p2=0.1, m3=0.4, p3=0.5

# final time
@ total=800
# set the plotting window size:
@ xlo=0, xhi=800, ylo=0, yhi=7000
@ bound=10000
@ maxstor=10000000

# run the simulation in the GUI by selecting (I)nitialconds|(G)o
# plot other species by selecting (G)raphic stuff|(A)dd curve and 
# assigning the y-axis

done