def plot_construct(ax, t, ymtet, ymlac, ymgamma, ytet, ylac, ygamma):
tind = int(t*10)
exp_lims = (1.0, 4.0)
ax.set_title('t = {}'.format(t), fontsize=8)
# Set color for each of the CDSs
tetr['opts']['color'] = [rescale(1 - expression(ymtet[tind], exp_lims), (1.0, 1.0)),
rescale(1 - expression(ymtet[tind], exp_lims), (0.75, 1.0)),
rescale(1 - expression(ymtet[tind], exp_lims), (0.17, 1.0))]
laci['opts']['color'] = [rescale(1 - expression(ymlac[tind], exp_lims), (0.38, 1.0)),
rescale(1 - expression(ymlac[tind], exp_lims), (0.82, 1.0)),
rescale(1 - expression(ymlac[tind], exp_lims), (0.32, 1.0))]
gamma['opts']['color'] = [rescale(1 - expression(ymgamma[tind], exp_lims), (0.38, 1.0)),
rescale(1 - expression(ymgamma[tind], exp_lims), (0.65, 1.0)),
rescale(1 - expression(ymgamma[tind], exp_lims), (0.87, 1.0))]
# Set transparency for each of the regulatory lines
lac_repress['opts']['color'] = [0.38, 0.82, 0.32,
rescale(repression(ylac[tind], 2.0, 8), (0.2, 1.0))]
gamma_repress['opts']['color'] = [0.38, 0.65, 0.87,
rescale(repression(ygamma[tind], 2.0, 8), (0.2, 1.0))]
tet_repress['opts']['color'] = [1.00, 0.75, 0.17,
rescale(repression(ytet[tind], 2.0, 8), (0.2, 1.0))]
# Set width for each of the regulatory lines
lac_repress['opts']['linewidth'] = rescale(repression(ylac[tind], 2.0, 8), (0.5, 2.0))
gamma_repress['opts']['linewidth'] = rescale(repression(ygamma[tind], 2.0, 8), (0.5, 2.0))
tet_repress['opts']['linewidth'] = rescale(repression(ytet[tind], 2.0, 8), (0.5, 2.0))
dnaplotlib.plot_sbol_designs([ax], [[plac, rbs1, tetr, term1, pgamma, rbs2, laci, term2, ptet, rbs3, gamma, term3]],
[[lac_repress, gamma_repress, tet_repress]])
ax.set_ylim([-10, 31])
def plot_construct(ax, t, ymtet, ymlac, ymgamma, ytet, ylac, ygamma):
tind = int(t*10)
exp_lims = (1.0, 4.0)
ax.set_title('t = {}'.format(t), fontsize=8)
# Set color for each of the CDSs
tetr['opts']['color'] = [rescale(1 - expression(ymtet[tind], exp_lims), (1.0, 1.0)),
rescale(1 - expression(ymtet[tind], exp_lims), (0.75, 1.0)),
rescale(1 - expression(ymtet[tind], exp_lims), (0.17, 1.0))]
laci['opts']['color'] = [rescale(1 - expression(ymlac[tind], exp_lims), (0.38, 1.0)),
rescale(1 - expression(ymlac[tind], exp_lims), (0.82, 1.0)),
rescale(1 - expression(ymlac[tind], exp_lims), (0.32, 1.0))]
gamma['opts']['color'] = [rescale(1 - expression(ymgamma[tind], exp_lims), (0.38, 1.0)),
rescale(1 - expression(ymgamma[tind], exp_lims), (0.65, 1.0)),
rescale(1 - expression(ymgamma[tind], exp_lims), (0.87, 1.0))]
# Set transparency for each of the regulatory lines
lac_repress['opts']['color'] = [0.38, 0.82, 0.32,
rescale(repression(ylac[tind], 2.0, 8), (0.2, 1.0))]
gamma_repress['opts']['color'] = [0.38, 0.65, 0.87,
rescale(repression(ygamma[tind], 2.0, 8), (0.2, 1.0))]
tet_repress['opts']['color'] = [1.00, 0.75, 0.17,
rescale(repression(ytet[tind], 2.0, 8), (0.2, 1.0))]
# Set width for each of the regulatory lines
lac_repress['opts']['linewidth'] = rescale(repression(ylac[tind], 2.0, 8), (0.5, 2.0))
gamma_repress['opts']['linewidth'] = rescale(repression(ygamma[tind], 2.0, 8), (0.5, 2.0))
tet_repress['opts']['linewidth'] = rescale(repression(ytet[tind], 2.0, 8), (0.5, 2.0))
dnaplotlib.plot_sbol_designs([ax], [[plac, rbs1, tetr, term1, pgamma, rbs2, laci, term2, ptet, rbs3, gamma, term3]],
[[lac_repress, gamma_repress, tet_repress]])
ax.set_ylim([-10, 31])
def main():
t = np.arange(0, 30.1, 0.1)
ymtet, ymlac, ymgamma, ytet, ylac, ygamma = zip(*odeint(repressilator, initial, t))
plt.close()
plt.figure(figsize=(3.5, 6.5))
gs = gridspec.GridSpec(8, 1, height_ratios=[1, 2.5, 0.1, 1, 1, 1, 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]])
ax.set_ylim([-10, 31])
# Plot of repressilator dynamics
ax = plt.subplot(gs[1])
plt.plot(t, ytet, color=[1.00, 0.75, 0.17])
plt.plot(t, ylac, color=[0.38, 0.82, 0.32])
plt.plot(t, ygamma, color=[0.38, 0.65, 0.87])
plt.axvline(x=1, color='k', linewidth=0.7)
plt.axvline(x=12, color='k', linewidth=0.7)
plt.axvline(x=25.3, color='k', linewidth=0.7)
plt.axvline(x=27.3, color='k', linewidth=0.7)
plt.axvline(x=29.4, color='k', linewidth=0.7)
plt.ylim([1,4])
ax.tick_params(axis='both', labelsize=8, width=0.8, length=3)
ax.yaxis.tick_left()
ax.xaxis.tick_bottom()
ax.set_xlabel('Time', fontsize=8, labelpad=1)
ax.set_ylabel('Protein Concentration', fontsize=8, labelpad=2)
plt.legend(['tetR', 'lacI', 'gamma'], frameon=False, fontsize=8, labelspacing=0.15, loc=(0.06,0.65))
# Plot of each timepoint
ax = plt.subplot(gs[3])
plot_construct(ax, 1, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[4])
plot_construct(ax, 12, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[5])
plot_construct(ax, 25.3, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[6])
plot_construct(ax, 27.3, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[7])
plot_construct(ax, 29.4, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
plt.subplots_adjust(hspace=0.4, left=0.12, right=0.95, top=0.99, bottom=0.01)
plt.savefig('repressilator_animate.pdf', transparent=True)
plt.savefig('repressilator_animate.png', dpi=300)
movie(t, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
def main():
plt.close()
plt.figure(figsize=(3.5, 1.5))
gs = gridspec.GridSpec(1, 1, height_ratios=[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]])
ax.set_ylim([-10, 31])
# Update subplot spacing
plt.subplots_adjust(hspace=0.4, left=0.12, right=0.95, top=0.99, bottom=0.01)
# Save the figure
plt.savefig('repressilator_animate.pdf', transparent=True)
plt.savefig('repressilator_animate.png', dpi=300)
def main():
t = np.arange(0, 30.1, 0.1)
ymtet, ymlac, ymgamma, ytet, ylac, ygamma = zip(
*odeint(repressilator, initial, t))
plt.close()
plt.figure(figsize=(3.5, 6.5))
gs = gridspec.GridSpec(8, 1, height_ratios=[1, 2.5, 0.1, 1, 1, 1, 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]])
ax.set_ylim([-10, 31])
# Plot of repressilator dynamics
ax = plt.subplot(gs[1])
plt.plot(t, ytet, color=[1.00, 0.75, 0.17])
plt.plot(t, ylac, color=[0.38, 0.82, 0.32])
plt.plot(t, ygamma, color=[0.38, 0.65, 0.87])
plt.axvline(x=1, color='k', linewidth=0.7)
plt.axvline(x=12, color='k', linewidth=0.7)
plt.axvline(x=25.3, color='k', linewidth=0.7)
plt.axvline(x=27.3, color='k', linewidth=0.7)
plt.axvline(x=29.4, color='k', linewidth=0.7)
plt.ylim([1, 4])
ax.tick_params(axis='both', labelsize=8, width=0.8, length=3)
ax.yaxis.tick_left()
ax.xaxis.tick_bottom()
ax.set_xlabel('Time', fontsize=8, labelpad=1)
ax.set_ylabel('Protein Concentration', fontsize=8, labelpad=2)
plt.legend(['tetR', 'lacI', 'gamma'],
frameon=False,
fontsize=8,
labelspacing=0.15,
loc=(0.06, 0.65))
# Plot of each timepoint
ax = plt.subplot(gs[3])
plot_construct(ax, 1, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[4])
plot_construct(ax, 12, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[5])
plot_construct(ax, 25.3, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[6])
plot_construct(ax, 27.3, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
ax = plt.subplot(gs[7])
plot_construct(ax, 29.4, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)
# Update subplot spacing
plt.subplots_adjust(hspace=0.4,
left=0.12,
right=0.95,
top=0.99,
bottom=0.01)
# Save the figure
plt.savefig('repressilator_animate.pdf', transparent=True)
plt.savefig('repressilator_animate.png', dpi=300)
# Generate the movie frames
movie(t, ymtet, ymlac, ymgamma, ytet, ylac, ygamma)