How to use tellurium - 10 common examples

# coding: utf-8

# Back to the main [Index](../index.ipynb)

# #### Draw diagram

# In[1]:

#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te

r = te.loada('''
model feedback()
   // Reactions:http://localhost:8888/notebooks/core/tellurium_export.ipynb#
   J0: $X0 -> S1; (VM1 * (X0 - S1/Keq1))/(1 + X0 + S1 +   S4^h);
   J1: S1 -> S2; (10 * S1 - 2 * S2) / (1 + S1 + S2);
   J2: S2 -> S3; (10 * S2 - 2 * S3) / (1 + S2 + S3);
   J3: S3 -> S4; (10 * S3 - 2 * S4) / (1 + S3 + S4);
   J4: S4 -> $X1; (V4 * S4) / (KS4 + S4);

  // Species initializations:
  S1 = 0; S2 = 0; S3 = 0;
  S4 = 0; X0 = 10; X1 = 0;

  // Variable initialization:
  VM1 = 10; Keq1 = 10; h = 10; V4 = 2.5; KS4 = 0.5;
end''')

model myModel
  S1 -> S2; k1*S1
  S1 = 10; S2 = 0
  k1 = 1
end
'''

phrasedml = '''
  model1 = model "myModel"
  sim1 = simulate uniform(0, 5, 100)
  task1 = run sim1 on model1
  plot "Figure 1" time vs S1, S2
'''

# create an experiment
exp = te.experiment(antimony, phrasedml)
# execute it
exp.execute(phrasedml)
# print python code
exp.printPython(phrasedml)


# ### OneStep
# Running a one step simulation.

# In[4]:

import tellurium as te

antimonyStr = '''
// Created by libAntimony v2.9
model *oneStep()

// Other declarations:
const compartment_, J0_v0, J1_k3, J2_k1, J2_k_1, J2_c, J2_q, J3_k2;
end
'''

phrasedmlStr = '''
model1 = model "parameterScan1D"
timecourse1 = simulate uniform(0, 20, 1000)
task0 = run timecourse1 on model1
task1 = repeat task0 for J0_v0 in [8, 4, 0.4], reset=true
plot task1.time vs task1.S1, task1.S2
'''

# phrasedml experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
exp.execute(phrasedmlStr)


# ### parameterScan2D
# 2D parameter scan

# In[6]:

import tellurium as te

antimonyStr = '''
// Created by libAntimony v2.9
model *parameterScan2D()

  // Compartments and Species:
  compartment compartment_;

end
"""

phrasedmlStr = """
    model0 = model "case_02"
    model1 = model model0 with S1=5.0
    sim0 = simulate uniform(0, 6, 100)
    task0 = run sim0 on model1
    task1 = repeat task0 for k1 in uniform(0.0, 5.0, 5), reset = true
    plot "Repeated task with reset" task1.time vs task1.S1, task1.S2
    plot "Repeated task varying k1" task1.k1 vs task1.S1
    # report task1.time vs task1.S1, task1.S2
"""

# phrasedml experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
exp.execute(phrasedmlStr)


# ### outputPlot3D
# Oscillations of MAPK pathway.

# In[9]:

import tellurium as te

antimonyStr = '''
// Created by libAntimony v2.9
model *case_09()

// Compartments and Species:
compartment compartment_;

model myModel
  S1 -> S2; k1*S1
  S1 = 10; S2 = 0
  k1 = 1
end
'''

phrasedml = '''
  model1 = model "myModel"
  sim1 = simulate uniform(0, 5, 100)
  task1 = run sim1 on model1
  plot "Figure 1" time vs S1, S2
'''

# create an experiment
exp = te.experiment(antimony, phrasedml)
# execute it
exp.execute(phrasedml)
# print python code
exp.printPython(phrasedml)


# ### OneStep
# Running a one step simulation.

# In[4]:

import tellurium as te

antimonyStr = '''
// Created by libAntimony v2.9
model *oneStep()

end
"""

phrasedmlStr = """
    model0 = model "case_02"
    model1 = model model0 with S1=5.0
    sim0 = simulate uniform(0, 6, 100)
    task0 = run sim0 on model1
    task1 = repeat task0 for k1 in uniform(0.0, 5.0, 5), reset = true
    plot "Repeated task with reset" task1.time vs task1.S1, task1.S2
    plot "Repeated task varying k1" task1.k1 vs task1.S1
    # report task1.time vs task1.S1, task1.S2
"""

# phrasedml experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
exp.execute(phrasedmlStr)


# ### outputPlot3D
# Oscillations of MAPK pathway.

# In[9]:

import tellurium as te

antimonyStr = '''
// Created by libAntimony v2.9
model *case_09()

// Compartments and Species:
compartment compartment_;

J2_q = 3;
J3_k2 = 5;

// Other declarations:
const compartment_, J0_v0, J1_k3, J2_k1, J2_k_1, J2_c, J2_q, J3_k2;
end
'''
p_str = '''
model1 = model "parameterScan1D"
timecourse1 = simulate uniform(0, 20, 1000)
task0 = run timecourse1 on model1
task1 = repeat task0 for J0_v0 in [8, 4, 0.4], reset=true
plot task1.time vs task1.S1, task1.S2
'''

run_case(os.path.realpath(__file__), a_str, p_str)

J9_KK10 = 15;

  // Other declarations:
  const compartment_, J0_V1, J0_Ki, J0_n, J0_K1, J1_V2, J1_KK2, J2_k3, J2_KK3;
  const J3_k4, J3_KK4, J4_V5, J4_KK5, J5_V6, J5_KK6, J6_k7, J6_KK7, J7_k8;
  const J7_KK8, J8_V9, J8_KK9, J9_V10, J9_KK10;
end
'''
p_str = '''
model1 = model "MAPKcascade"
sim1 = simulate uniform(0,4000,1000)
task1 = run sim1 on model1
plot task1.time vs task1.MAPK, task1.MAPK_P, task1.MAPK_PP
'''

run_case(os.path.realpath(__file__), a_str, p_str)

// Other declarations:
  const J0_VM1, J0_Keq1, J0_h, J4_V4, J4_KS4;
''')

# time vector
result = r.simulate (0, 20, 201, ['time'])

h_values = [r.J0_h + k for k in range(0,8)]
for h in h_values:
    r.reset()
    r.J0_h = h
    m = r.simulate(0, 20, 201, ['S1'])
    result = numpy.hstack([result, m])
    
te.plotArray(result, labels=['h={}'.format(int(h)) for h in h_values]);


# ### Compare simulations

# In[14]:

import tellurium as te

r = te.loada ('''
     v1: $Xo -> S1;  k1*Xo;
     v2: S1 -> $w;   k2*S1;

     //initialize.  Deterministic process.
     k1 = 1; k2 = 1; S1 = 20; Xo = 1;
''')

def test_loada(self):
        rr = te.loada('''
            model example0
              S1 -> S2; k1*S1
              S1 = 10
              S2 = 0
              k1 = 0.1
            end
        ''')
        self.assertIsNotNone(rr.getModel())