Animating pathway

Here is an example of runnign a simulation and plotting the results as an animation. The model is a 20 step linear pathway where at time zero, all concentrations are zero. The boundary species Xo is set to 10 and as the simualtion runs the species slowly fill up to their steady-state levels. We can capture the data and turn it intot an animation using the matplotlib.animation from matlpotlib. At the end we convert the frames into a mp4 file. I generated the model using hte buildnetworks class in teUtils

import tellurium as te
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation, FFMpegFileWriter

r = te.loada('''
J1: $Xo -> S1; e1*(k10*Xo - k11*S1); 
J2: S1 -> S2; e2*(k20*S1 - k21*S2); 
J3: S2 -> S3; e3*(k30*S2 - k31*S3); 
J4: S3 -> S4; e4*(k40*S3 - k41*S4); 
J5: S4 -> S5; e5*(k50*S4 - k51*S5); 
J6: S5 -> S6; e6*(k60*S5 - k61*S6); 
J7: S6 -> S7; e7*(k70*S6 - k71*S7); 
J8: S7 -> S8; e8*(k80*S7 - k81*S8); 
J9: S8 -> S9; e9*(k90*S8 - k91*S9); 
J10: S9 -> S10; e10*(k100*S9 - k101*S10); 
J11: S10 -> S11; e11*(k110*S10 - k111*S11); 
J12: S11 -> S12; e12*(k120*S11 - k121*S12); 
J13: S12 -> S13; e13*(k130*S12 - k131*S13); 
J14: S13 -> S14; e14*(k140*S13 - k141*S14); 
J15: S14 -> S15; e15*(k150*S14 - k151*S15); 
J16: S15 -> S16; e16*(k160*S15 - k161*S16); 
J17: S16 -> S17; e17*(k170*S16 - k171*S17); 
J18: S17 -> S18; e18*(k180*S17 - k181*S18); 
J19: S18 -> S19; e19*(k190*S18 - k191*S19); 
J20: S19 -> $X1; e20*(k200*S19 - k201*X1); 

k10 = 0.86;  k11 = 0.24
e1= 1; k20 = 2.24;  k21 = 0.51
e2= 1; k30 = 2.00;  k31 = 0.49
e3= 1; k40 = 2.54;  k41 = 0.83
e4= 1; k50 = 3.05;  k51 = 0.97
e5= 1; k60 = 1.29;  k61 = 0.10
e6= 1; k70 = 1.94;  k71 = 0.20
e7= 1; k80 = 3.01;  k81 = 0.17
e8= 1; k90 = 0.64;  k91 = 0.19
e9= 1; k100 = 1.96;  k101 = 0.42
e10= 1; k110 = 2.47;  k111 = 0.63
e11= 1; k120 = 4.95;  k121 = 0.51
e12= 1; k130 = 4.78;  k131 = 0.70
e13= 1; k140 = 3.77;  k141 = 0.78
e14= 1; k150 = 1.93;  k151 = 0.37
e15= 1; k160 = 3.87;  k161 = 0.96
e16= 1; k170 = 0.83;  k171 = 0.37
e17= 1; k180 = 1.82;  k181 = 0.69
e18= 1; k190 = 2.62;  k191 = 0.83
e19= 1; k200 = 4.85;  k201 = 0.67
e20= 1; Xo = 10.00
X1 = 0
S1 = 0; S2 = 0; S3 = 0; S4 = 0; 
S5 = 0; S6 = 0; S7 = 0; S8 = 0; 
S9 = 0; S10 = 0; S11 = 0; S12 = 0; 
S13 = 0; S14 = 0; S15 = 0; S16 = 0; 
S17 = 0; S18 = 0; S19 = 0; 
''')

# I'm running this on windows so I had to install the ffmpeg binary
# in order to save the video as an mp4 file
# for more info go tot his page:
# https://suryadayn.medium.com/error-requested-moviewriter-ffmpeg-not-available-easy-fix-9d1890a487d3
plt.rcParams['animation.ffmpeg_path'] ="C:\\ffmpeg\\bin\\ffmpeg.exe"

endTime = 18
fig, ax = plt.subplots(figsize=(8, 5))
ax.set(xlim=(-1, r.getNumIndFloatingSpecies()), ylim=(0, 18))

m = r.simulate(0, endTime, 100)

label = ax.text(15.6, 19, 'Time=', ha='center', va='center', fontsize=18, color="Black")
bars = ax.bar(r.getFloatingSpeciesIds(), m[0,1:], color='b', alpha = 0.5)
    
  def barAnimate(i):
    label.set_text('Time = ' + f'{m[i,0]:.2f}')

    for bar, h in zip(bars, m[i,1:]):
        bar.set_color ('r')
        bar.set_height(h)

anim = FuncAnimation(fig, barAnimate, interval=50, frames=100, repeat=False)

# You can save themp4 file anywhere you want
anim.save('c:\\tmp\\animation.mp4', fps=30)

plt.draw()
plt.show()

This is the resulting video: