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()
SSA_builder.SSA_MM('Cell'+str(indx)+'_Reaction3','vd',
km=['kd'],Rct=['Pc'+index])
#The complexing four:
SSA_builder.SSA_MA_cytonuc('Cell'+str(indx)+'_Reaction4','Pc'+index,
'Pn'+index,'k1_','k2_')
return SSAmodel,state_names,param_names
if __name__=='__main__':
print param
ODEsolC = ctb.CircEval(ODEmodel(), param, y0in)
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)
fn.setOption("name", "kiss_oscillator_2011")
return fn
if __name__ == "__main__":
"""
Test suite for the model. We will run with both casadi deterministic
and gillespy stochastic simulations.
"""
import circadiantoolbox as ctb
import PlotOptions as plo
# create deterministic circadian object
kiss_odes = ctb.CircEval(kiss_model_ode(), param, y0in)
kiss_odes.burnTransient_sim()
kiss_odes.intODEs_sim(200)
# plot deterministic solutions
plo.PlotOptions()
plt.figure()
plt.plot(kiss_odes.ts, kiss_odes.sol[:, 0], label='e1, V oscillatory')
plt.plot(kiss_odes.ts, kiss_odes.sol[:, 2], label='e2')
plt.title('High-Freq. Signal Propagates as described by TF')
plt.xlabel('t')
plt.ylabel('e')
plt.legend(loc=0)
plt.tight_layout(**plo.layout_pad)
# fft setup data
return fn
if __name__ == "__main__":
import circadiantoolbox as ctb
import PlotOptions as plo
from numpy import fft
import pdb
#param[1]=0
#param[2]=0
# create deterministic circadian object
coupled_odes = ctb.CircEval(ODEmodel(), param, y0in)
#coupled_odes.burnTransient_sim()
coupled_odes.intODEs_sim(200)
#Fixing signal to show perturbation
coupled_odes.sol[:, 8] = coupled_odes.sol[:, 8] + amp * np.sin(
freq * coupled_odes.ts)
plo.PlotOptions()
"""
plt.plot(coupled_odes.ts, coupled_odes.sol[:,8],label='C1P 1')
plt.plot(coupled_odes.ts, coupled_odes.sol[:,3], label='vip 1')
plt.plot(coupled_odes.ts, coupled_odes.sol[:,18], label = 'VIP 2')
plt.plot(coupled_odes.ts, coupled_odes.sol[:,21], label = 'CREB 2')
plt.plot(coupled_odes.ts, coupled_odes.sol[:,11], label = 'per 2')
plt.plot(coupled_odes.ts, coupled_odes.sol[:,0], label = 'per 1')