mhjensen
28 lines
659 B
Python
28 lines
659 B
Python
import numpy as np
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data = np.loadtxt('ecoli.csv', delimiter=',')
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t_experiment = data[:,0]
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N_experiment = data[:,1]
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def error(p):
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r = p[0]
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T = 1200 # cell can divide after T sec
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t_max = 5*T # 5 generations in experiment
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t = np.linspace(0, t_max, len(t_experiment))
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dt = (t[1] - t[0])
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N = np.zeros(t.size)
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N[0] = 100
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for n in range(0, len(t)-1, 1):
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N[n+1] = N[n] + r*dt*N[n]
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e = np.sqrt(np.sum((N - N_experiment)**2))/N[0] # error measure
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e = abs(N[-1] - N_experiment[-1])/N[0]
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print 'r=', r, 'e=',e
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return e
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from scipy.optimize import minimize
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p = minimize(error, [0.0006], tol=1E-5)
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print p
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