# file deterministic_vilar_oscillator.ode
# deterministic simulation of genetic oscillator
# from Vilar et al. (2002) PNAS 99 5988-5992.
# problem 7.8.27

#parameters
par ga=250 
par ba=5
par Ka=0.5 
par alpha0=0.1
par da=1
par kc=200
par gr=50 
par br=10
par Kr=1
par dr=0.1

#model equations
A' = ba*(ga/ba)*(alpha0+(A/Ka))/(1+(A/Ka)) - da*A - kc*A*R
R' = br*(gr/br)*((A/Kr))/(1+(A/Kr)) - dr*R - kc*A*R + da*C
C' = kc*A*R - da*C

# initial condition
init A=5, R=10, C=35

# final time
@ total=50
# set the plotting window size:
@ xlo=0, xhi=50, ylo=0, yhi=250
@ bound=1000
@ dt=0.00005
@ 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