def main():
#Creates SSA version of model.
SSAmodel,state_names,param_names=StochModel()
#calls and runs stochkit
trajectories = stk.stochkit(SSAmodel,job_id='test',t=75,number_of_trajectories=100,increment=0.1)
#evaluation bit
StochEval = stk.StochEval(trajectories,state_names,param_names,vol)
StochEval.PlotAvg('p',color='blue')
pl.show()
pdb.set_trace()
def main():
#Creates SSA version of model.
ODEmodel, SSAmodel, state_names, param_names = FullModel(True)
ODEsol = ctb.CircEval(ODEmodel, param, y0in)
y0LC = ODEsol.burnTransient_sim(tf=000, numsteps=1000)
sol = ODEsol.intODEs_sim(y0LC, 10, numsteps=1000)
tsol = ODEsol.ts
pdb.set_trace()
trajectories = stk.stochkit(SSAmodel,
job_id='tyson',
t=10,
number_of_trajectories=100,
increment=0.1)
StochEval = stk.StochEval(trajectories, state_names, param_names, vol)
StochEval.PlotAvg('X', color='red', traces=True)
StochEval.PlotAvg('Y', color='black', traces=True)
pl.plot(tsol, vol * sol)
pl.show()
pdb.set_trace()
sol = ODEsolC.intODEs_sim(100)
tsol = ODEsolC.ts
plt.plot(sol)
plt.show()
tf=10
inc = 0.05
adjacency = np.array([[1,1,0],[0,1,1],[0,0,1]])#,
#[0,0.5,0.5,0],
#[0,0,0.5,0],
#[0,0,0,0]])
SSAnet,state_names,param_names = SSAnetwork(ODEmodel(),
y0in,param,adjacency)
pdb.set_trace()
traj = stk.stochkit(SSAnet,job_id='threestate',t=tf,
number_of_trajectories=1,increment=inc,
seed=11)
plt.plot(traj[:,1:])
pass
#find where we should rewire
rewire = (np.random.rand(len(locs[0])) <= beta)
for i in xrange(len(rewire)):
if rewire[i] == True:
#remove conn1
adjacency[locs[0][i],locs[1][i]] = 0
adjacency[np.random.randint(cellcount),locs[1][i]] = 1
plt.imshow(ring)
plt.figure()
plt.imshow(adjacency)
pdb.set_trace()
SSAnet,state_names,param_names = SSAnetwork(ODEmodel(),
y0in,param,adjacency)
traj = stk.stochkit(SSAnet,job_id='beta0.1_network',t=tf,
number_of_trajectories=1,increment=inc,
seed=11)
plt.plot(traj[0][:,1:])
pass