ets.py

from models import *
from scipy.integrate import odeint
import matplotlib.pyplot as plt

"""
    TESTING
"""

# simulation parameters
t_end = 200
N = 1000

# model parameters
alpha1 = 34.73  # protein_production
alpha2 = 49.36  # protein_production
alpha3 = 32.73  # protein_production
alpha4 = 49.54  # protein_production
delta1 = 1.93  # protein_degradation
delta2 = 0.69  # protein_degradation
Kd = 10.44  # Kd
n = 4.35  # hill

params_ff = (alpha1, alpha2, alpha3, alpha4, delta1, delta2, Kd, n)

# three-bit counter with external clock
# a1, not_a1, q1, not_q1, a2, not_a2, q2, not_q2, a3, not_a3, q3, not_q3
Y0 = np.array([0] * 12)  # initial state
T = np.linspace(0, t_end, N)  # vector of timesteps

# numerical interation
Y = odeint(three_bit_model, Y0, T, args=(params_ff,))

Y_reshaped = np.split(Y, Y.shape[1], 1)

# plotting the results
Q1 = Y_reshaped[2]
not_Q1 = Y_reshaped[3]
Q2 = Y_reshaped[6]
not_Q2 = Y_reshaped[7]
Q3 = Y_reshaped[10]
not_Q3 = Y_reshaped[11]

plt.plot(T, Q1, label='q1')
plt.plot(T, Q2, label='q2')
plt.plot(T, Q3, label='q3')
# plt.plot(T, not_Q1, label='not q1')
# plt.plot(T, not_Q2, label='not q2')

plt.plot(T, get_clock(T), '--', linewidth=2, label="CLK", color='black', alpha=0.25)

plt.legend()
plt.show()