Branch: master
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
45 lines (35 sloc) 1.06 KB
"""Hello PySB! (i.e. hello world) A simple model with a reversible binding rule.
(This is the example shown on the home page.)
from __future__ import print_function
from pysb import *
# Declare the monomers
Monomer('L', ['s'])
Monomer('R', ['s'])
# Declare the parameters
Parameter('L_0', 100)
Parameter('R_0', 200)
Parameter('kf', 1e-3)
Parameter('kr', 1e-3)
# Declare the initial conditions
Initial(L(s=None), L_0)
Initial(R(s=None), R_0)
# Declare the binding rule
Rule('L_binds_R', L(s=None) + R(s=None) | L(s=1) % R(s=1), kf, kr)
# Observe the complex
Observable('LR', L(s=1) % R(s=1))
if __name__ == '__main__':
from numpy import linspace
from matplotlib.pyplot import plot, xlabel, ylabel, show
from pysb.simulator import ScipyOdeSimulator
# Simulate the model through 40 seconds
time = linspace(0, 40, 100)
x = ScipyOdeSimulator(model).run(tspan=time).all
# Plot the trajectory of LR
plot(time, x['LR'])
xlabel('Time (seconds)')
ylabel('Amount of LR')