def cell_cycle_sim(time):
exp_time = 0
sim = SSA(gnxp_reactions,init_state)
while exp_time < time:
exp_time += replication_time
sim.run(exp_time) # run until exp_time
new_state = [rbinom(n,division_prob) if n > 0 else 0
for n in sim.state]
sim.state = new_state
print exp_time
return sim
from ssa import SSA
kr = 1/100.0
gr = 10**4
kp = 500 * gr
gp = 6.79 #approx H_500 (harmonic number)
k3 = 10**6
gnxp_reactions = [((1,0,0),kr), #mRNA production
((-1,0,0),gr), #mRNA degradation
((-1,0,1),kp), #protein complex formation
((1,1,-1),k3), #protein formation we do things this way
#to pack everything into mass action kinetics
((0,-1,0),gp), #protein degradation
]
init_state = (0,0,0)
gnxp_sim = SSA(gnxp_reactions,init_state)
gnxp_sim.verbose = True
gnxp_sim.run(1000)
print "loaded"