In [18]:
%matplotlib inline
import numpy as np
from scipy.integrate import odeint
import dnaplotlib
import matplotlib.pyplot as plt
from matplotlib import gridspec
In [19]:
# Initialize Parts
# tetr  is orange [1.00, 0.75, 0.17]
# lacI  is green  [0.38, 0.82, 0.32]
# gamma is blue   [0.38, 0.65, 0.87]
plac = {'name':'P_lac', 'start':1, 'end':10, 'type':'Promoter', 'opts': {'color':[0.38, 0.82, 0.32]}}
rbs1 = {'name':'RBS', 'start':11, 'end':20, 'type':'RBS', 'opts':{'linewidth': 0, 'color':[0.0, 0.0, 0.0]}}
tetr = {'name':'tetR', 'start':21, 'end':40, 'type':'CDS', 'opts':{'label': 'tetR', 'fontsize': 8,  'label_y_offset': 0, 'label_x_offset': -2, 'label_style':'italic', 'color':[1.00, 0.75, 0.17]}}
term1 = {'name':'Term', 'start':41, 'end':55, 'type':'Terminator'}
pgamma = {'name':'P_gamma', 'start':56, 'end':65, 'type':'Promoter', 'opts': {'color':[0.38, 0.65, 0.87]}}
rbs2 = {'name':'RBS', 'start':66, 'end':75, 'type':'RBS', 'opts':{'linewidth': 0, 'color':[0.0, 0.0, 0.0]}}
laci = {'name':'lacI', 'start':76, 'end':95, 'type':'CDS', 'opts':{'label': 'lacI', 'fontsize': 8,  'label_y_offset': 0, 'label_x_offset': -2, 'label_style':'italic', 'color':[0.38, 0.82, 0.32]}}
term2 = {'name':'Term', 'start':96, 'end':110, 'type':'Terminator'}
ptet = {'name':'P_tet', 'start':111, 'end':120, 'type':'Promoter', 'opts': {'color':[1.00, 0.75, 0.17]}}
rbs3 = {'name':'RBS', 'start':121, 'end':130, 'type':'RBS', 'opts':{'linewidth': 0, 'color':[0.0, 0.0, 0.0]}}
gamma = {'name':'gamma', 'start':131, 'end':150, 'type':'CDS', 'opts':{'label': 'gamma', 'fontsize': 8, 'label_y_offset': 0, 'label_x_offset': -1, 'label_style':'italic', 'color':[0.38, 0.65, 0.87]}}
term3 = {'name':'Term', 'start':151, 'end':165, 'type':'Terminator'}

lac_repress = {'from_part':laci, 'to_part':plac, 'type':'Repression', 'opts':{'linewidth':1, 'color':[0.38, 0.82, 0.32]}}
gamma_repress = {'from_part':gamma, 'to_part':pgamma, 'type':'Repression', 'opts':{'linewidth':1, 'color':[0.38, 0.65, 0.87]}}
tet_repress = {'from_part':tetr, 'to_part':ptet, 'type':'Repression', 'opts':{'linewidth':1, 'color':[1.00, 0.75, 0.17]}}
In [38]:
plt.figure(figsize=(4, 2),dpi=300)
gs = gridspec.GridSpec(1, 1)

# Plot of repressilator circuit
ax = plt.subplot(gs[0])
dnaplotlib.plot_sbol_designs([ax], [[plac, rbs1, tetr, term1, pgamma, rbs2, laci, term2, ptet, rbs3, gamma, term3]],
                             [[lac_repress, gamma_repress, tet_repress]])
Out[38]:
(216.0, [-2.16, 218.16], [-35, 35])
In [ ]: