"""
Example showing basic timecourse simulations and plotting.
"""
from sbmlsim.plot.plotting_matplotlib import plt
from sbmlsim.simulation import Timecourse, TimecourseSim
from sbmlsim.simulator import SimulatorSerial as Simulator
from sbmlsim.test import MODEL_REPRESSILATOR
[docs]def run_timecourse_examples():
"""Run various timecourses."""
simulator = Simulator(MODEL_REPRESSILATOR)
# 1. simple timecourse simulation
print("*** simple timecourse ***")
tc_sim = TimecourseSim(Timecourse(start=0, end=100, steps=100))
xr1 = simulator.run_timecourse(tc_sim)
print(tc_sim)
# 2. timecourse with parameter changes
print("*** parameter change ***")
tc_sim = TimecourseSim(
Timecourse(start=0, end=100, steps=100, changes={"X": 10, "Y": 200})
)
xr2 = simulator.run_timecourse(tc_sim)
print(tc_sim)
# 3. combined timecourses
print("*** combined timecourse ***")
tc_sim = TimecourseSim(
[
Timecourse(start=0, end=100, steps=100),
Timecourse(start=0, end=100, steps=100, changes={"X": 10, "Y": 20}),
]
)
xr3 = simulator.run_timecourse(tc_sim)
print(tc_sim)
# create figure
fig, (ax1, ax2, ax3) = plt.subplots(nrows=1, ncols=3, figsize=(15, 5))
fig.subplots_adjust(wspace=0.3, hspace=0.3)
ax1.set_title("simple timecourse")
ax2.set_title("parameter change")
ax3.set_title("combined timecourse")
for xres, ax in [(xr1, ax1), (xr2, ax2), (xr3, ax3)]:
ax.plot(xres.time, xres.X, label="X")
ax.plot(xres.time, xres.Y, label="Y")
ax.plot(xres.time, xres.Z, label="Z")
for ax in (ax1, ax2, ax3):
ax.legend()
ax.set_xlabel("time")
ax.set_ylabel("concentration")
plt.show()
if __name__ == "__main__":
run_timecourse_examples()